Publications by authors named "Jatmiko"

35 Publications

Using niche construction theory to generate testable foraging hypotheses at Liang Bua.

Evol Anthropol 2021 Jan 2;30(1):8-16. Epub 2021 Feb 2.

Pusat Penelitian Arkeologi Nasional, Jakarta, Indonesia.

Niche construction theory (NCT) has emerged as a promising theoretical tool for interpreting zooarchaeological material. However, its juxtaposition against more established frameworks like optimal foraging theory (OFT) has raised important criticism around the testability of NCT for interpreting hominin foraging behavior. Here, we present an optimization foraging model with NCT features designed to consider the destructive realities of the archaeological record after providing a brief review of OFT and NCT. Our model was designed to consider a foragers decision to exploit an environment given predation risk, mortality, and payoff ratios between different ecologies, like more-open or more-forested environments. We then discuss how the model can be used with zooarchaeological data for inferring environmental exploitation by a primitive hominin, Homo floresiensis, from the island of Flores in Southeast Asia. Our example demonstrates that NCT can be used in combination with OFT principles to generate testable foraging hypotheses suitable for zooarchaeological research.
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http://dx.doi.org/10.1002/evan.21884DOI Listing
January 2021

Physicochemical and sensory properties of terasi (an Indonesian fermented shrimp paste) produced using Lactobacillus plantarum and Bacillus amyloliquefaciens.

Microbiol Res 2021 Jan 9;242:126619. Epub 2020 Oct 9.

Department of Nutrition, Faculty of Medicine, Brawijaya University, Jl. Veteran Malang, East Java, Indonesia.

Terasi is an Indonesian shrimp paste that is traditionally fermented and is widely consumed by Indonesian people. Terasi is produced by utilizing endogenous bacteria from raw materials as starters. Due to the variation in endogenous bacteria during production, terasi of varying quality is produced. The objectives of this study were to investigate the effects of starters on the physicochemical and sensory properties of terasi. The effects of individual or combination inoculation of Lactobacillus plantarum SB7 and Bacillus amyloliquefaciens BC9 were compared to those of noninoculation during a two-week period of terasi production. The starters darkened the color of the terasi. The terasi produced with the starters had higher protein contents (62.93-64.80 %) than those of the noninoculated terasi (63.66-65.80 %). Although proteolysis was weakly affected by the starters, the starters reduced the terasi fermentation period. The combination starter inoculation resulted in a high glutamic acid level (44284.8 ± 231.22 mg/kg). Volatile alcohols were more abundant in the starter-inoculated terasi than in the noninoculated terasi. Assessments of the sensory parameters by panelists suggested a preference for inoculated terasi. In conclusion, the addition of starters (L. plantarum SB7 and B. amyloliquefaciens BC9) in terasi production improved the physicochemical and sensory properties of the terasi.
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http://dx.doi.org/10.1016/j.micres.2020.126619DOI Listing
January 2021

Mitogenomics of macaques (Macaca) across Wallace's Line in the context of modern human dispersals.

J Hum Evol 2020 09 8;146:102852. Epub 2020 Aug 8.

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.

Wallace's Line demarcates a biogeographical boundary between the Indomalaya and Australasian ecoregions. Most placental mammalian genera, for example, occur to the west of this line, whereas most marsupial genera occur to the east. However, macaque monkeys are unusual because they naturally occur on both western and eastern sides. To further explore this anomalous distribution, we analyzed 222 mitochondrial genomes from ∼20 macaque species, including new genomes from 60 specimens. These comprise a population sampling of most Sulawesi macaques, Macaca fascicularis (long-tailed macaques) specimens that were collected by Alfred R. Wallace and specimens that were recovered during archaeological excavations at Liang Bua, a cave on the Indonesian island of Flores. In M. fascicularis, three mitochondrial lineages span the southernmost portion of Wallace's Line between Bali and Lombok, and divergences within these lineages are contemporaneous with, and possibly mediated by, past dispersals of modern human populations. Near the central portion of Wallace's Line between Borneo and Sulawesi, a more ancient dispersal of macaques from mainland Asia to Sulawesi preceded modern human colonization, which was followed by rapid dispersal of matrilines and was subsequently influenced by recent interspecies hybridization. In contrast to previous studies, we find no strong signal of recombination in most macaque mitochondrial genomes. These findings further characterize macaque evolution before and after modern human dispersal throughout Southeast Asia and point to possible effects on biodiversity of ancient human cultural diasporas.
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http://dx.doi.org/10.1016/j.jhevol.2020.102852DOI Listing
September 2020

Dataset of vehicle images for Indonesia toll road tariff classification.

Data Brief 2020 Oct 23;32:106061. Epub 2020 Jul 23.

Faculty of Computer Science, Universitas Indonesia, Indonesia.

Vehicle classifications with different methods have been applied for many purposes. The data provided in this article is useful for classifying vehicle purposes following the Indonesia toll road tariffs. Indonesia toll road tariff regulations divide vehicles into five groups as follows, group-1, group-2, group-3, group-4, and group-5, respectively. Group-1 is a class of non-truck vehicles, while group-2 to group-5 are classes of truck vehicles. The non-truck class consists of the sedan, pick-up, minibus, bus, MPV, and SUV. Truck classes are grouped based on the number of truck's axles. Group-2 is a class of trucks with two axles, a group-3 truck with three axles, a group-4 truck with four axles, and a group-5 truck with five axles or more. The dataset is categorized into five classes accordingly, which are group-1, group-2, group-3, group-4, and group-5 images. The data made available in this article observes images of vehicles obtained using a smartphone camera. The vehicle images dataset incorporated with deep learning, transfer learning, fine-tuning, and the Residual Neural Network (ResNet) model can yield exceptional results in the classification of vehicles by the number of axles.
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http://dx.doi.org/10.1016/j.dib.2020.106061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394761PMC
October 2020

Dataset of short-term prediction of CO concentration based on a wireless sensor network.

Data Brief 2020 Aug 25;31:105924. Epub 2020 Jun 25.

Faculty of Computer Science, Universitas Indonesia, Kampus UI Depok, Indonesia.

This CO data is gathered from WSN (Wireless Sensor Network) sensors that is placed in some areas. To make this observation framework run effectively, examining the relationships between factors is required. We can utilize multiple wireless sensor devices. There are three parts of the system, including the sensor device, the sink node device, and the server. We use those devices to acquire data over a three-month period. In terms of the server infrastructure, we utilized an application server, a user interface server, and a database server to store our data. This study built a WSN framework for CO observations. We investigate, analyze, and predict the level of CO, and the results have been collected. The Random Forest algorithm achieved a 0.82 R2 Score.
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http://dx.doi.org/10.1016/j.dib.2020.105924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358660PMC
August 2020

Implementation of geographical information systems for the study of diseases caused by vector-borne arboviruses in Southeast Asia: A review based on the publication record.

Geospat Health 2020 06 17;15(1). Epub 2020 Jun 17.

Centre for Remote Sensing and Geographical Information System (PUSPICS), Universitas Gadjah Mada, Sekip Utara, Yogyakarta.

The spread of mosquito-borne diseases in Southeast Asia has dramatically increased in the latest decades. These infections include dengue, chikungunya and Japanese Encephalitis (JE), high-burden viruses sharing overlapping disease manifestation and vector distribution. The use of Geographical Information Systems (GIS) to monitor the dynamics of disease and vector distribution can assist in disease epidemic prediction and public health interventions, particularly in Southeast Asia where sustained high temperatures drive the epidemic spread of these mosquito-borne viruses. Due to lack of accurate data, the spatial and temporal dynamics of these mosquito-borne viral disease transmission countries are poorly understood, which has limited disease control effort. By following studies carried out on these three viruses across the region in a specific time period revealing general patterns of research activities and characteristics, this review finds the need to improve decision-support by disease mapping and management. The results presented, based on a publication search with respect to diseases due to arboviruses, specifically dengue, chikungunya and Japanese encephalitis, should improve opportunities for future studies on the implementation of GIS in the control of mosquito-borne viral diseases in Southeast Asia.
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http://dx.doi.org/10.4081/gh.2020.862DOI Listing
June 2020

Optimization of glutaminase-free L-asparaginase production using mangrove endophytic B27.

F1000Res 2019 20;8:1938. Epub 2019 Nov 20.

Department of Biology, Faculty of Natural Science and Mathematic, Brawijaya University, Malang, East Java, 65145, Indonesia.

The mangrove, , an essential source of endophytic bacteria, was investigated for its ability to produce glutaminase-free L-asparaginase. The study aimed to obtain glutaminase-free L-asparaginase-producing endophytic bacteria from the mangrove and to optimize enzyme production. The screening of L-asparaginase-producing bacteria used modified M9 medium. The potential producer was further analyzed with respect to its species using 16S rRNA gene sequencing. Taguchi experimental design was applied to optimize the enzyme production. Four factors (L-asparagine concentration, pH, temperature, and inoculum concentration) were selected at four levels. The results indicated that the endophytic bacteria B27 isolated from was a potential producer of glutaminase-free L-asparaginase. The experiment indicated that pH 6, temperature at 35°C, and inoculum concentration of 1.5% enabled the best production and were essential factors. L-asparagine (2%) was less critical for optimum production. Conclusions: L. fusiformis B27, isolated from , can be optimized for L-ASNase enzyme production using optimization factors (L-ASNase, pH, temperature, and inoculum), which can increase L-ASNase enzyme production by approximately three-fold.
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http://dx.doi.org/10.12688/f1000research.21178.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287513PMC
July 2020

Autochthonous Acid-Producing Bacteria from Catfish ( sp.) with Antibacterial Activity against Selected Fish Pathogens: A Preliminary Study.

Int J Microbiol 2020 21;2020:8526581. Epub 2020 Feb 21.

Coastal and Marine Science Center, Brawijaya University. Jl. Veteran, 65145 East Java, Indonesia.

In this study, the application of an autochthonous microorganism as probiotic on catfish ( sp.) was scarcely reported. This study aimed to obtain probiotic candidates from the digestive tract (intestinal and gastric) of catfish. A total of nine isolates were successfully isolated from the catfish. Almost all bacterial colonies were morphologically round, had flat edges, were yellow, and produced clear zones as a sign of producing acid during culture. The analysis showed that the three isolates had the best activity in inhibiting fish pathogen isolates. Furthermore, molecular analysis revealed that those three isolates were UB-C1, UB-C5, and UB-C8. Interestingly, those three bacteria were non-lactic acid bacteria.
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http://dx.doi.org/10.1155/2020/8526581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068145PMC
February 2020

Combined organic biomarker and use-wear analyses of stone artefacts from Liang Bua, Flores, Indonesia.

Sci Rep 2019 11 26;9(1):17553. Epub 2019 Nov 26.

Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia.

Organic biomarker and lithic use-wear analyses of archaeological implements manufactured and/or used by hominins in the past offers a means of assessing how prehistoric peoples utilised natural resources. Currently, most studies focus on one of these techniques, rather than using both in sequence. This study aims to assess the potential of combining both methods to analyse stone artefacts, using a set of 69 stones excavated from the cave site of Liang Bua (Flores, Indonesia). Prior to chemical analysis, an initial inspection of the artefacts revealed potential use-wear traces but no visible residues. Gas chromatography mass spectrometry (GC-MS) analysis, including the targeting of 86 lipids, terpenes, terpenoids, alkanes and their analogues, found compounds with plant or animal origin on 27 of the 69 stones. The artefacts were subsequently cleaned, and use-wear analysis identified traces of use on 43 artefacts. Use-wear analysis confirmed traces of use on 23 of the 27 artefacts with potential use-residues that were determined by GC-MS. The GC-MS results were broadly consistent with the functional classes identified in the later use-wear analysis. This inclusive approach for stone artefact analysis strengthens the identifications made through multiple lines of enquiry. There remain conflicts and uncertainties in specific cases, suggesting the need for further refinement and analyses of the relationships between use-wear and residues.
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http://dx.doi.org/10.1038/s41598-019-53782-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879511PMC
November 2019

Temporal shifts in the distribution of murine rodent body size classes at Liang Bua (Flores, Indonesia) reveal new insights into the paleoecology of Homo floresiensis and associated fauna.

J Hum Evol 2019 05 14;130:45-60. Epub 2019 Mar 14.

Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia 5005, Australia; School of Biological Sciences, Environment Institute, and Centre for Applied Conservation Science, University of Adelaide, Adelaide, South Australia 5005 Australia.

Liang Bua, the type locality of Homo floresiensis, is a limestone cave located in the western part of the Indonesian island of Flores. The relatively continuous stratigraphic sequence of the site spans the past ∼190 kyr and contains ∼275,000 taxonomically identifiable vertebrate skeletal elements, ∼80% of which belong to murine rodent taxa (i.e., rats). Six described genera are present at Liang Bua (Papagomys, Spelaeomys, Hooijeromys, Komodomys, Paulamys, and Rattus), one of which, Hooijeromys, is newly recorded in the site deposits, being previously known only from Early to Middle Pleistocene sites in central Flores. Measurements of the proximal femur (n = 10,212) and distal humerus (n = 1186) indicate five murine body size classes ranging from small (mouse-sized) to giant (common rabbit-sized) are present. The proportions of these five classes across successive stratigraphic units reveal two major changes in murine body size distribution due to significant shifts in the abundances of more open habitat-adapted medium-sized murines versus more closed habitat-adapted smaller-sized ones. One of these changes suggests a modest increase in available open habitats occurred ∼3 ka, likely the result of anthropogenic changes to the landscape related to farming by modern human populations. The other and more significant change occurred ∼60 ka suggesting a rapid shift from more open habitats to more closed conditions at this time. The abrupt reduction of medium-sized murines, along with the disappearance of H. floresiensis, Stegodon florensis insularis (an extinct proboscidean), Varanus komodoensis (Komodo dragon), Leptoptilos robustus (giant marabou stork), and Trigonoceps sp. (vulture) at Liang Bua ∼60-50 ka, is likely the consequence of these animals preferring and tracking more open habitats to elsewhere on the island. If correct, then the precise timing and nature of the extinction of H. floresiensis and its contemporaries must await new discoveries at Liang Bua or other as yet unexcavated sites on Flores.
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http://dx.doi.org/10.1016/j.jhevol.2019.02.002DOI Listing
May 2019

Comparing Compliance and Efficacy of Isocaloric Oral Nutritional Supplementation Using 1.5 kcal/mL or 1 kcal/mL Sip Feeds in Mildly to Moderately Malnourished Indonesian Children: A Randomized Controlled Trial.

Pediatr Gastroenterol Hepatol Nutr 2018 Oct 10;21(4):315-320. Epub 2018 Oct 10.

Department of Child Health, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.

Purpose: This study set out to evaluate the compliance to, and efficacy of oral supplementation, using a 1.5 kcal/mL or 1 kcal/mL sip feed, in children with mild to moderate malnutrition.

Methods: This was a parallel, randomized, controlled open-label trial in children aged 3 to 6 years with a weight for height Z (WHZ) score <-1 and ≥-3, who were randomized to receive a total of 600 kcal/day from either a 1.5 kcal/mL or a 1.0 kcal/mL pediatric sip feed for 28 days. Assessments included daily study product intake, body weight, tolerance and dietary intake from solid food.

Results: Of 110 children recruited, 98 (mean±standard deviation of age 49±7 months) completed the study. Both sip feeds were well tolerated, with high compliance (80±24% and 81±22% of prescribed volume in 1.5 kcal/mL and 1.0 kcal/mL groups respectively, =0.79). Both study groups gained similar weight during the 28 days intervention period (0.42±0.40 kg in 1.5 kcal/mL group vs. 0.49±0.49 kg in 1.0 kcal/mL group, =0.43). There were no significant differences between the groups in weight gain and in the change in WHZ score over the intervention period. Dietary analysis at the end of the study did not show replacement of solid food by the oral nutritional supplements.

Conclusion: In children with mild to moderate malnutrition, both 1.5 kcal/mL and 1 kcal/mL pediatric sip feeds had high compliance and were well tolerated, and were equally effective in promoting weight gain in the 28 days study period.
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http://dx.doi.org/10.5223/pghn.2018.21.4.315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182471PMC
October 2018

The spatio-temporal distribution of archaeological and faunal finds at Liang Bua (Flores, Indonesia) in light of the revised chronology for Homo floresiensis.

J Hum Evol 2018 11 31;124:52-74. Epub 2018 Aug 31.

Centre for Archaeological Science, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia.

Liang Bua, the type site of Homo floresiensis, is a limestone cave on the Indonesian island of Flores with sedimentary deposits currently known to range in age from about 190 thousand years (ka) ago to the present. Recent revision of the stratigraphy and chronology of this depositional sequence suggests that skeletal remains of H. floresiensis are between ∼100 and 60 ka old, while cultural evidence of this taxon occurs until ∼50 ka ago. Here we examine the compositions of the faunal communities and stone artifacts, by broad taxonomic groups and raw materials, throughout the ∼190 ka time interval preserved in the sequence. Major shifts are observed in both the faunal and stone artifact assemblages that reflect marked changes in paleoecology and hominin behavior, respectively. Our results suggest that H. floresiensis and Stegodon florensis insularis, along with giant marabou stork (Leptoptilos robustus) and vulture (Trigonoceps sp.), were likely extinct by ∼50 ka ago. Moreover, an abrupt and statistically significant shift in raw material preference due to an increased use of chert occurs ∼46 thousand calibrated radiocarbon (C) years before present (ka cal. BP), a pattern that continues through the subsequent stratigraphic sequence. If an increased preference for chert does, in fact, characterize Homo sapiens assemblages at Liang Bua, as previous studies have suggested (e.g., Moore et al., 2009), then the shift observed here suggests that modern humans arrived on Flores by ∼46 ka cal. BP, which would be the earliest cultural evidence of modern humans in Indonesia.
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http://dx.doi.org/10.1016/j.jhevol.2018.07.001DOI Listing
November 2018

A reassessment of the early archaeological record at Leang Burung 2, a Late Pleistocene rock-shelter site on the Indonesian island of Sulawesi.

PLoS One 2018 11;13(4):e0193025. Epub 2018 Apr 11.

Centre for Archaeological Science, School of Earth & Environmental Sciences, University of Wollongong, Wollongong, New South Wales, Australia.

This paper presents a reassessment of the archaeological record at Leang Burung 2, a key early human occupation site in the Late Pleistocene of Southeast Asia. Excavated originally by Ian Glover in 1975, this limestone rock-shelter in the Maros karsts of Sulawesi, Indonesia, has long held significance in our understanding of early human dispersals into 'Wallacea', the vast zone of oceanic islands between continental Asia and Australia. We present new stratigraphic information and dating evidence from Leang Burung 2 collected during the course of our excavations at this site in 2007 and 2011-13. Our findings suggest that the classic Late Pleistocene modern human occupation sequence identified previously at Leang Burung 2, and proposed to span around 31,000 to 19,000 conventional 14C years BP (~35-24 ka cal BP), may actually represent an amalgam of reworked archaeological materials. Sources for cultural materials of mixed ages comprise breccias from the rear wall of the rock-shelter-remnants of older, eroded deposits dated to 35-23 ka cal BP-and cultural remains of early Holocene antiquity. Below the upper levels affected by the mass loss of Late Pleistocene deposits, our deep-trench excavations uncovered evidence for an earlier hominin presence at the site. These findings include fossils of now-extinct proboscideans and other 'megafauna' in stratified context, as well as a cobble-based stone artifact technology comparable to that produced by late Middle Pleistocene hominins elsewhere on Sulawesi.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0193025PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894965PMC
July 2018

Late Pleistocene songbirds of Liang Bua (Flores, Indonesia); the first fossil passerine fauna described from Wallacea.

PeerJ 2017 17;5:e3676. Epub 2017 Aug 17.

Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany.

Background: Passerines (Aves: Passeriformes) dominate modern terrestrial bird communities yet their fossil record is limited. Liang Bua is a large cave on the Indonesian island of Flores that preserves Late Pleistocene-Holocene deposits (∼190 ka to present day). Birds are the most diverse faunal group at Liang Bua and are present throughout the stratigraphic sequence.

Methods: We examined avian remains from the Late Pleistocene deposits of Sector XII, a 2 × 2 m area excavated to about 8.5 m depth. Although postcranial passerine remains are typically challenging to identify, we found several humeral characters particularly useful in discriminating between groups, and identified 89 skeletal elements of passerines.

Results: At least eight species from eight families are represented, including the Large-billed Crow ( cf. ) the Australasian Bushlark () a friarbird ( sp.), and the Pechora Pipit ( cf. )

Discussion: These remains constitute the first sample of fossil passerines described in Wallacea. Two of the taxa no longer occur on Flores today; a large sturnid (cf. ) and a grassbird ( sp.). Palaeoecologically, the songbird assemblage suggests open grassland and tall forests, which is consistent with conditions inferred from the non-passerine fauna at the site. cf. , found in the -bearing layers, was likely part of a scavenging guild that fed on carcasses of alongside vultures ( sp.), giant storks (), komodo dragons (), and probably as well.
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http://dx.doi.org/10.7717/peerj.3676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5563437PMC
August 2017

Effects of Supernatants from Escherichia coli Nissle 1917 and Faecalibacterium prausnitzii on Intestinal Epithelial Cells and a Rat Model of 5-Fluorouracil-Induced Mucositis.

Nutr Cancer 2017 Feb-Mar;69(2):307-318. Epub 2017 Jan 17.

a School of Animal and Veterinary Sciences , University of Adelaide , Adelaide , South Australia , Australia.

Faecalibacterium prausnitzii (Fp) and Escherichia coli Nissle 1917 (EcN) are probiotics, which have been reported to ameliorate certain gastrointestinal disorders. We evaluated the effects of supernatants (SN) derived from Fp and EcN on 5-fluorouracil (5-FU)-treated intestinal cells and in a rat model of mucositis. In vitro: IEC-6, Caco-2, and T-84 cells were analyzed for viability and monolayer permeability. In vivo: Female dark agouti rats were gavaged with Fp or EcN SN and injected intraperitoneally with saline (control) or 5-FU to induce mucositis. Rats were euthanized and intestinal tissues collected for myeloperoxidase assay and histological analyses. In vitro: Caco-2 cell viability was further reduced when treated with Fp SN + 5-FU compared to 5-FU controls. In both Caco-2 and T-84 cells, Fp SN partially prevented the decrease in transepithelial electrical resistance (TER) caused by 5-FU administration. In vivo: 5-FU-injected rats administered Fp SN or EcN SN partly prevented body weight loss and normalized water intake compared to 5-FU controls. These results suggest a growth inhibitory mechanism of Fp SN action on transformed epithelial cells that could be mediated by effects on tight junctions. Factors derived from Fp SN and EcN SN could have a role in reducing the severity of intestinal mucositis.
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http://dx.doi.org/10.1080/01635581.2017.1263747DOI Listing
January 2018

Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia.

Nature 2016 Apr 30;532(7599):366-9. Epub 2016 Mar 30.

Centre for Archaeological Science, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia.

Homo floresiensis, a primitive hominin species discovered in Late Pleistocene sediments at Liang Bua (Flores, Indonesia), has generated wide interest and scientific debate. A major reason this taxon is controversial is because the H. floresiensis-bearing deposits, which include associated stone artefacts and remains of other extinct endemic fauna, were dated to between about 95 and 12 thousand calendar years (kyr) ago. These ages suggested that H. floresiensis survived until long after modern humans reached Australia by ~50 kyr ago. Here we report new stratigraphic and chronological evidence from Liang Bua that does not support the ages inferred previously for the H. floresiensis holotype (LB1), ~18 thousand calibrated radiocarbon years before present (kyr cal. BP), or the time of last appearance of this species (about 17 or 13-11 kyr cal. BP). Instead, the skeletal remains of H. floresiensis and the deposits containing them are dated to between about 100 and 60 kyr ago, whereas stone artefacts attributable to this species range from about 190 to 50 kyr in age. Whether H. floresiensis survived after 50 kyr ago--potentially encountering modern humans on Flores or other hominins dispersing through southeast Asia, such as Denisovans--is an open question.
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http://dx.doi.org/10.1038/nature17179DOI Listing
April 2016

Unique Dental Morphology of Homo floresiensis and Its Evolutionary Implications.

PLoS One 2015 18;10(11):e0141614. Epub 2015 Nov 18.

Centre for Archaeological Science, University of Wollongong, Wollongong, Australia.

Homo floresiensis is an extinct, diminutive hominin species discovered in the Late Pleistocene deposits of Liang Bua cave, Flores, eastern Indonesia. The nature and evolutionary origins of H. floresiensis' unique physical characters have been intensively debated. Based on extensive comparisons using linear metric analyses, crown contour analyses, and other trait-by-trait morphological comparisons, we report here that the dental remains from multiple individuals indicate that H. floresiensis had primitive canine-premolar and advanced molar morphologies, a combination of dental traits unknown in any other hominin species. The primitive aspects are comparable to H. erectus from the Early Pleistocene, whereas some of the molar morphologies are more progressive even compared to those of modern humans. This evidence contradicts the earlier claim of an entirely modern human-like dental morphology of H. floresiensis, while at the same time does not support the hypothesis that H. floresiensis originated from a much older H. habilis or Australopithecus-like small-brained hominin species currently unknown in the Asian fossil record. These results are however consistent with the alternative hypothesis that H. floresiensis derived from an earlier Asian Homo erectus population and experienced substantial body and brain size dwarfism in an isolated insular setting. The dentition of H. floresiensis is not a simple, scaled-down version of earlier hominins.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141614PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651360PMC
June 2016

New wrist bones of Homo floresiensis from Liang Bua (Flores, Indonesia).

J Hum Evol 2013 Feb 4;64(2):109-29. Epub 2013 Jan 4.

Department of Anatomical Sciences, Stony Brook University, Health Sciences Center T-8 040, Stony Brook, NY 11794-8081, USA.

The carpals from the Homo floresiensis type specimen (LB1) lack features that compose the shared, derived complex of the radial side of the wrist in Neandertals and modern humans. This paper comprises a description and three-dimensional morphometric analysis of new carpals from at least one other individual at Liang Bua attributed to H. floresiensis: a right capitate and two hamates. The new capitate is smaller than that of LB1 but is nearly identical in morphology. As with capitates from extant apes, species of Australopithecus, and LB1, the newly described capitate displays a deeply-excavated nonarticular area along its radial aspect, a scaphoid facet that extends into a J-hook articulation on the neck, and a more radially-oriented second metacarpal facet; it also lacks an enlarged palmarly-positioned trapezoid facet. Because there is no accommodation for the derived, palmarly blocky trapezoid that characterizes Homo sapiens and Neandertals, this individual most likely had a plesiomorphically wedge-shaped trapezoid (like LB1). Morphometric analyses confirm the close similarity of the new capitate and that of LB1, and are consistent with previous findings of an overall primitive articular geometry. In general, hamate morphology is more conserved across hominins, and the H. floresiensis specimens fall at the far edge of the range of variation for H. sapiens in a number of metrics. However, the hamate of H. floresiensis is exceptionally small and exhibits a relatively long, stout hamulus lacking the oval-shaped cross-section characteristic of human and Neandertal hamuli (variably present in australopiths). Documentation of a second individual with primitive carpal anatomy from Liang Bua, along with further analysis of trapezoid scaling relative to the capitate in LB1, refutes claims that the wrist of the type specimen represents a modern human with pathology. In total, the carpal anatomy of H. floresiensis supports the hypothesis that the lineage leading to the evolution of this species originated prior to the cladogenetic event that gave rise to modern humans and Neandertals.
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http://dx.doi.org/10.1016/j.jhevol.2012.10.003DOI Listing
February 2013

Craniofacial morphology of Homo floresiensis: description, taxonomic affinities, and evolutionary implication.

J Hum Evol 2011 Dec 28;61(6):644-82. Epub 2011 Oct 28.

Department of Anthropology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba-shi, Ibaraki Prefecture Japan.

This paper describes in detail the external morphology of LB1/1, the nearly complete and only known cranium of Homo floresiensis. Comparisons were made with a large sample of early groups of the genus Homo to assess primitive, derived, and unique craniofacial traits of LB1 and discuss its evolution. Principal cranial shape differences between H. floresiensis and Homo sapiens are also explored metrically. The LB1 specimen exhibits a marked reductive trend in its facial skeleton, which is comparable to the H. sapiens condition and is probably associated with reduced masticatory stresses. However, LB1 is craniometrically different from H. sapiens showing an extremely small overall cranial size, and the combination of a primitive low and anteriorly narrow vault shape, a relatively prognathic face, a rounded oval foramen that is greatly separated anteriorly from the carotid canal/jugular foramen, and a unique, tall orbital shape. Whereas the neurocranium of LB1 is as small as that of some Homo habilis specimens, it exhibits laterally expanded parietals, a weak suprameatal crest, a moderately flexed occipital, a marked facial reduction, and many other derived features that characterize post-habilis Homo. Other craniofacial characteristics of LB1 include, for example, a relatively narrow frontal squama with flattened right and left sides, a marked frontal keel, posteriorly divergent temporal lines, a posteriorly flexed anteromedial corner of the mandibular fossa, a bulbous lateral end of the supraorbital torus, and a forward protruding maxillary body with a distinct infraorbital sulcus. LB1 is most similar to early Javanese Homo erectus from Sangiran and Trinil in these and other aspects. We conclude that the craniofacial morphology of LB1 is consistent with the hypothesis that H. floresiensis evolved from early Javanese H. erectus with dramatic island dwarfism. However, further field discoveries of early hominin skeletal remains from Flores and detailed analyses of the finds are needed to understand the evolutionary history of this endemic hominin species.
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http://dx.doi.org/10.1016/j.jhevol.2011.08.008DOI Listing
December 2011

Preface: research at Liang Bua, Flores, Indonesia.

J Hum Evol 2009 Nov 5;57(5):437-49. Epub 2009 Sep 5.

GeoQuEST Research Centre, University of Wollongong, NSW, Australia.

Excavations at Liang Bua, Flores, Indonesia, have yielded evidence for an endemic human species, Homo floresiensis, a population that occupied the cave between approximately 95-17ka. This discovery has major implications for early hominin evolution and dispersal in Africa and Asia, attracting worldwide interest. This preface describes the rationale for the excavations in historical, geographical, and wider research contexts, as well as the methods used. It also introduces the other papers on aspects of Liang Bua research that feature in this edition of the Journal of Human Evolution.
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http://dx.doi.org/10.1016/j.jhevol.2009.07.003DOI Listing
November 2009

Homo floresiensis: a cladistic analysis.

J Hum Evol 2009 Nov 23;57(5):623-39. Epub 2009 Jul 23.

Australian National University, Canberra, ACT, Australia.

The announcement of a new species, Homo floresiensis, a primitive hominin that survived until relatively recent times is an enormous challenge to paradigms of human evolution. Until this announcement, the dominant paradigm stipulated that: 1) only more derived hominins had emerged from Africa, and 2) H. sapiens was the only hominin since the demise of Homo erectus and Homo neanderthalensis. Resistance to H. floresiensis has been intense, and debate centers on two sets of competing hypotheses: 1) that it is a primitive hominin, and 2) that it is a modern human, either a pygmoid form or a pathological individual. Despite a range of analytical techniques having been applied to the question, no resolution has been reached. Here, we use cladistic analysis, a tool that has not, until now, been applied to the problem, to establish the phylogenetic position of the species. Our results produce two equally parsimonious phylogenetic trees. The first suggests that H. floresiensis is an early hominin that emerged after Homo rudolfensis (1.86Ma) but before H. habilis (1.66Ma, or after 1.9Ma if the earlier chronology for H. habilis is retained). The second tree indicates H. floresiensis branched after Homo habilis.
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http://dx.doi.org/10.1016/j.jhevol.2009.05.002DOI Listing
November 2009

Continuities in stone flaking technology at Liang Bua, Flores, Indonesia.

J Hum Evol 2009 Nov 10;57(5):503-26. Epub 2009 Apr 10.

University of New England, Armidale, New South Wales, Australia.

This study examines trends in stone tool reduction technology at Liang Bua, Flores, Indonesia, where excavations have revealed a stratified artifact sequence spanning 95k.yr. The reduction sequence practiced throughout the Pleistocene was straightforward and unchanging. Large flakes were produced off-site and carried into the cave where they were reduced centripetally and bifacially by four techniques: freehand, burination, truncation, and bipolar. The locus of technological complexity at Liang Bua was not in knapping products, but in the way techniques were integrated. This reduction sequence persisted across the Pleistocene/Holocene boundary with a minor shift favoring unifacial flaking after 11ka. Other stone-related changes occurred at the same time, including the first appearance of edge-glossed flakes, a change in raw material selection, and more frequent fire-induced damage to stone artifacts. Later in the Holocene, technological complexity was generated by "adding-on" rectangular-sectioned stone adzes to the reduction sequence. The Pleistocene pattern is directly associated with Homo floresiensis skeletal remains and the Holocene changes correlate with the appearance of Homo sapiens. The one reduction sequence continues across this hominin replacement.
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http://dx.doi.org/10.1016/j.jhevol.2008.10.006DOI Listing
November 2009

Brief communication: "Pathological" deformation in the skull of LB1, the type specimen of Homo floresiensis.

Am J Phys Anthropol 2009 Sep;140(1):177-85

Department of Anthropology, National Museum of Nature and Science, Tokyo 169-0073, Japan.

If the holotype of Homo floresiensis, LB1, suffered from a severe developmental pathology, this could undermine its status as the holotype of a new species. One of the proposed pathological indicators that still remains untested is asymmetric distortion in the skull of LB1 (Jacob et al.: Proc Natl Acad Sci USA 103 (2006) 13421-13426). Here, we present evidence that LB1 exhibits antemortem craniofacial deformities that are consistent with posterior deformational (positional) plagiocephaly. This is a relatively common condition in modern people with no serious associated health problems and does not represent a severe developmental abnormality in LB1.
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http://dx.doi.org/10.1002/ajpa.21066DOI Listing
September 2009

The type specimen (LB1) of Homo floresiensis did not have Laron syndrome.

Am J Phys Anthropol 2009 Sep;140(1):52-63

Department of Anthropology, Florida State University, Tallahassee, FL 32306-7772, USA.

The type specimen (LB1) of Homo floresiensis has been hypothesized to be a pathological human afflicted with Laron Syndrome (LS), a type of primary growth hormone insensitivity (Hershkovitz et al.: Am J Phys Anthropol 134 [2007] 198-208). Comparing measurements, photographs and three-dimensional, computed-tomography reconstructions of LB1 with data and diagnoses from the literature on LS, we critically evaluate numerous skull and postcranial traits that Hershkovitz et al. identified as being shared by LB1 and patients with LS. The statements regarding most of these traits are new to the clinical literature and lack quantitative support. LB1 and patients with LS differ markedly in the size and shape of the cranium; thickness and pneumatization of cranial bones; morphology of the face, mandible, teeth, and chin; form of the shoulder, wrist, and pelvis; and general body proportions including relative foot size. Claims that patients with LS are similar to LB1 in displaying protracted scapulae, short clavicles, low degrees of humeral torsion, flaring ilia, and curved tibiae are not supported by data or corroborating images. Some points of similarity (e.g., femoral neck-shaft angle, femoral bicondylar angle, and estimated stature) can be found in other hominins, and cannot be considered diagnostic. From our review and analysis, we conclude that LB1 did not suffer from LS.
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http://dx.doi.org/10.1002/ajpa.21035DOI Listing
September 2009

Reconstructing the geomorphic history of Liang Bua, Flores, Indonesia: a stratigraphic interpretation of the occupational environment.

J Hum Evol 2009 Nov 9;57(5):465-83. Epub 2009 Mar 9.

GeoQuEST Research Centre, University of Wollongong, NSW, Australia.

Liang Bua, in Flores, Indonesia, was formed as a subterranean chamber over 600ka. From this time to the present, a series of geomorphic events influenced the structure of the cave and cave deposits, creating a complex stratigraphy. Within these deposits, nine main sedimentary units have been identified. The stratigraphic relationships between these units provide the evidence needed to reconstruct the geomorphic history of the cave. This history was dominated by water action, including slope wash processes, channel formation, pooling of water, and flowstone precipitation, which created waterfalls, cut-and-fill stratigraphy, large pools of water, and extensive flowstone cappings. The reconstructed sequence of events over the last 190k.yr. has been summarized by a series of time slices that demonstrate the nature of the occupational environment in Liang Bua. The earliest artifacts at the site, dated to approximately 190ka, testify to hominin presence in the area, but the reconstructions suggest that occupation of the cave itself may not have been possible until after approximately 100ka. At approximately 95ka, channel erosion of a basal unit, which displays evidence of deposition in a pond environment, created a greater relief on the cave floor, and formed remanent areas of higher ground that later became a focus for hominin occupation from 74-61ka by the west wall and in the center of the cave, and from approximately 18-17ka by the east wall. These zones have been identified according to the sloping nature of the stratigraphy and the distribution of artifacts, and their locations have implications for the archaeological interpretation of the site.
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http://dx.doi.org/10.1016/j.jhevol.2009.01.004DOI Listing
November 2009

LB1's virtual endocast, microcephaly, and hominin brain evolution.

J Hum Evol 2009 Nov 28;57(5):597-607. Epub 2009 Feb 28.

Department of Anthropology, Florida State University, Tallahassee, 32306, USA.

Earlier observations of the virtual endocast of LB1, the type specimen for Homo floresiensis, are reviewed, extended, and interpreted. Seven derived features of LB1's cerebral cortex are detailed: a caudally-positioned occipital lobe, lack of a rostrally-located lunate sulcus, a caudally-expanded temporal lobe, advanced morphology of the lateral prefrontal cortex, shape of the rostral prefrontal cortex, enlarged gyri in the frontopolar region, and an expanded orbitofrontal cortex. These features indicate that LB1's brain was globally reorganized despite its ape-sized cranial capacity (417cm(3)). Neurological reorganization may thus form the basis for the cognitive abilities attributed to H. floresiensis. Because of its tiny cranial capacity, some workers think that LB1 represents a Homo sapiens individual that was afflicted with microcephaly, or some other pathology, rather than a new species of hominin. We respond to concerns about our earlier study of microcephalics compared with normal individuals, and reaffirm that LB1 did not suffer from this pathology. The intense controversy about LB1 reflects an older continuing dispute about the relative evolutionary importance of brain size versus neurological reorganization. LB1 may help resolve this debate and illuminate constraints that governed hominin brain evolution.
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http://dx.doi.org/10.1016/j.jhevol.2008.10.008DOI Listing
November 2009

The primitive wrist of Homo floresiensis and its implications for hominin evolution.

Science 2007 Sep;317(5845):1743-5

Human Origins Program, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.

Whether the Late Pleistocene hominin fossils from Flores, Indonesia, represent a new species, Homo floresiensis, or pathological modern humans has been debated. Analysis of three wrist bones from the holotype specimen (LB1) shows that it retains wrist morphology that is primitive for the African ape-human clade. In contrast, Neandertals and modern humans share derived wrist morphology that forms during embryogenesis, which diminishes the probability that pathology could result in the normal primitive state. This evidence indicates that LB1 is not a modern human with an undiagnosed pathology or growth defect; rather, it represents a species descended from a hominin ancestor that branched off before the origin of the clade that includes modern humans, Neandertals, and their last common ancestor.
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http://dx.doi.org/10.1126/science.1147143DOI Listing
September 2007

Age and biostratigraphic significance of the Punung Rainforest Fauna, East Java, Indonesia, and implications for Pongo and Homo.

J Hum Evol 2007 Dec 13;53(6):709-17. Epub 2007 Aug 13.

GeoQuEST Research Centre, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, NSW 2522, Australia.

The Punung Fauna is a key component in the biostratigraphic sequence of Java. It represents the most significant faunal turnover on the island in the last 1.5 million years, when Stegodon and other archaic mammal species characteristic of earlier Faunal stages were replaced by a fully modern fauna that included rainforest-dependent species such as Pongo pygmaeus (orangutan). Here, we report the first numerical ages for the Punung Fauna obtained by luminescence and uranium-series dating of the fossil-bearing deposits and associated flowstones. The Punung Fauna contained in the dated breccia is of early Last Interglacial age (between 128+/-15 and 118+/-3 ka). This result has implications for the age of the preceding Ngandong Fauna, including Homo erectus remains found in the Ngandong Terrace, and for the timing of Homo sapiens arrival in Southeast Asia, in view of claims for a modern human tooth associated with the Punung breccia.
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http://dx.doi.org/10.1016/j.jhevol.2007.06.002DOI Listing
December 2007

Homo floresiensis and the evolution of the hominin shoulder.

J Hum Evol 2007 Dec 13;53(6):718-31. Epub 2007 Aug 13.

Anatomical Sciences, Stony Brook University School of Medicine, Stony Brook, NY, USA.

The holotype of Homo floresiensis, diminutive hominins with tiny brains living until 12,000 years ago on the island of Flores, is a partial skeleton (LB1) that includes a partial clavicle (LB1/5) and a nearly complete right humerus (LB1/50). Although the humerus appears fairly modern in most regards, it is remarkable in displaying only 110 degrees of humeral torsion, well below modern human average values. Assuming a modern human shoulder configuration, such a low degree of humeral torsion would result in a lateral set to the elbow. Such an elbow joint would function more nearly in a frontal than in a sagittal plane, and this is certainly not what anyone would have predicted for a tool-making Pleistocene hominin. We argue that Homo floresiensis probably did not have a modern human shoulder configuration: the clavicle was relatively short, and we suggest that the scapula was more protracted, resulting in a glenoid fossa that faced anteriorly rather than laterally. A posteriorly directed humeral head was therefore appropriate for maintaining a normally functioning elbow joint. Similar morphology in the Homo erectus Nariokotome boy (KNM-WT 15000) suggests that this shoulder configuration may represent a transitional stage in pectoral girdle evolution in the human lineage.
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http://dx.doi.org/10.1016/j.jhevol.2007.06.003DOI Listing
December 2007