Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave.

Genetic and fragmented palaeoanthropological data suggest that Denisovans were once widely distributed across eastern Eurasia1-3. Despite limited archaeological evidence, this indicates that Denisovans were capable of adapting to a highly diverse range of environments. Here we integrate zooarchaeological and proteomic analyses of the late Middle to Late Pleistocene faunal assemblage from Baishiya Karst Cave on the Tibetan Plateau, where a Denisovan mandible and Denisovan sedimentary mitochondrial DNA were found3,4. Using zooarchaeology by mass spectrometry, we identify a new hominin rib specimen that dates to approximately 48-32 thousand years ago (layer 3). Shotgun proteomic analysis taxonomically assigns this specimen to the Denisovan lineage, extending their presence at Baishiya Karst Cave well into the Late Pleistocene. Throughout the stratigraphic sequence, the faunal assemblage is dominated by Caprinae, together with megaherbivores, carnivores, small mammals and birds. The high proportion of anthropogenic modifications on the bone surfaces suggests that Denisovans were the primary agent of faunal accumulation. The chaîne opératoire of carcass processing indicates that animal taxa were exploited for their meat, marrow and hides, while bone was also used as raw material for the production of tools. Our results shed light on the behaviour of Denisovans and their adaptations to the diverse and fluctuating environments of the late Middle and Late Pleistocene of eastern Eurasia.

Evidence for the earliest structural use of wood at least 476,000 years ago.

Wood artefacts rarely survive from the Early Stone Age since they require exceptional conditions for preservation; consequently, we have limited information about when and how hominins used this basic raw material1. We report here on the earliest evidence for structural use of wood in the archaeological record. Waterlogged deposits at the archaeological site of Kalambo Falls, Zambia, dated by luminescence to at least 476 ± 23 kyr ago (ka), preserved two interlocking logs joined transversely by an intentionally cut notch. This construction has no known parallels in the African or Eurasian Palaeolithic. The earliest known wood artefact is a fragment of polished plank from the Acheulean site of Gesher Benot Ya'aqov, Israel, more than 780 ka (refs. 2,3). Wooden tools for foraging and hunting appear 400 ka in Europe4-8, China9 and possibly Africa10. At Kalambo we also recovered four wood tools from 390 ka to 324 ka, including a wedge, digging stick, cut log and notched branch. The finds show an unexpected early diversity of forms and the capacity to shape tree trunks into large combined structures. These new data not only extend the age range of woodworking in Africa but expand our understanding of the technical cognition of early hominins11, forcing re-examination of the use of trees in the history of technology12,13.

Reappraising the palaeobiology of Australopithecus.

The naming of Australopithecus africanus in 1925, based on the Taung Child, heralded a new era in human evolutionary studies and turned the attention of the then Eurasian-centric palaeoanthropologists to Africa, albeit with reluctance. Almost one hundred years later, Africa is recognized as the cradle of humanity, where the entire evolutionary history of our lineage prior to two million years ago took place-after the Homo-Pan split. This Review examines data from diverse sources and offers a revised depiction of the genus and characterizes its role in human evolution. For a long time, our knowledge of Australopithecus came from both A. africanus and Australopithecus afarensis, and the members of this genus were portrayed as bipedal creatures that did not use stone tools, with a largely chimpanzee-like cranium, a prognathic face and a brain slightly larger than that of chimpanzees. Subsequent field and laboratory discoveries, however, have altered this portrayal, showing that Australopithecus species were habitual bipeds but also practised arboreality; that they occasionally used stone tools to supplement their diet with animal resources; and that their infants probably depended on adults to a greater extent than what is seen in apes. The genus gave rise to several taxa, including Homo, but its direct ancestor remains elusive. In sum, Australopithecus had a pivotal bridging role in our evolutionary history owing to its morphological, behavioural and temporal placement between the earliest archaic putative hominins and later hominins-including the genus Homo.

Innovative ochre processing and tool use in China 40,000 years ago.

Homo sapiens was present in northern Asia by around 40,000 years ago, having replaced archaic populations across Eurasia after episodes of earlier population expansions and interbreeding1-4. Cultural adaptations of the last Neanderthals, the Denisovans and the incoming populations of H. sapiens into Asia remain unknown1,5-7. Here we describe Xiamabei, a well-preserved, approximately 40,000-year-old archaeological site in northern China, which includes the earliest known ochre-processing feature in east Asia, a distinctive miniaturized lithic assemblage with bladelet-like tools bearing traces of hafting, and a bone tool. The cultural assembly of traits at Xiamabei is unique for Eastern Asia and does not correspond with those found at other archaeological site assemblages inhabited by archaic populations or those generally associated with the expansion of H. sapiens, such as the Initial Upper Palaeolithic8-10. The record of northern Asia supports a process of technological innovations and cultural diversification emerging in a period of hominin hybridization and admixture2,3,6,11.

Protracted development of stick tool use skills extends into adulthood in wild western chimpanzees.

Tool use is considered a driving force behind the evolution of brain expansion and prolonged juvenile dependency in the hominin lineage. However, it remains rare across animals, possibly due to inherent constraints related to manual dexterity and cognitive abilities. In our study, we investigated the ontogeny of tool use in chimpanzees (Pan troglodytes), a species known for its extensive and flexible tool use behavior. We observed 70 wild chimpanzees across all ages and analyzed 1,460 stick use events filmed in the Taï National Park, Côte d'Ivoire during the chimpanzee attempts to retrieve high-nutrient, but difficult-to-access, foods. We found that chimpanzees increasingly utilized hand grips employing more than 1 independent digit as they matured. Such hand grips emerged at the age of 2, became predominant and fully functional at the age of 6, and ubiquitous at the age of 15, enhancing task accuracy. Adults adjusted their hand grip based on the specific task at hand, favoring power grips for pounding actions and intermediate grips that combine power and precision, for others. Highly protracted development of suitable actions to acquire hidden (i.e., larvae) compared to non-hidden (i.e., nut kernel) food was evident, with adult skill levels achieved only after 15 years, suggesting a pronounced cognitive learning component to task success. The prolonged time required for cognitive assimilation compared to neuromotor control points to selection pressure favoring the retention of learning capacities into adulthood.

Multiple hominin dispersals into Southwest Asia over the past 400,000 years.

Pleistocene hominin dispersals out of, and back into, Africa necessarily involved traversing the diverse and often challenging environments of Southwest Asia1-4. Archaeological and palaeontological records from the Levantine woodland zone document major biological and cultural shifts, such as alternating occupations by Homo sapiens and Neanderthals. However, Late Quaternary cultural, biological and environmental records from the vast arid zone that constitutes most of Southwest Asia remain scarce, limiting regional-scale insights into changes in hominin demography and behaviour1,2,5. Here we report a series of dated palaeolake sequences, associated with stone tool assemblages and vertebrate fossils, from the Khall Amayshan 4 and Jubbah basins in the Nefud Desert. These findings, including the oldest dated hominin occupations in Arabia, reveal at least five hominin expansions into the Arabian interior, coinciding with brief 'green' windows of reduced aridity approximately 400, 300, 200, 130-75 and 55 thousand years ago. Each occupation phase is characterized by a distinct form of material culture, indicating colonization by diverse hominin groups, and a lack of long-term Southwest Asian population continuity. Within a general pattern of African and Eurasian hominin groups being separated by Pleistocene Saharo-Arabian aridity, our findings reveal the tempo and character of climatically modulated windows for dispersal and admixture.

3.3 million years of stone tool complexity suggests that cumulative culture began during the Middle Pleistocene.

Cumulative culture, the accumulation of modifications, innovations, and improvements over generations through social learning, is a key determinant of the behavioral diversity across Homo sapiens populations and their ability to adapt to varied ecological habitats. Generations of improvements, modifications, and lucky errors allow humans to use technologies and know-how well beyond what a single naive individual could invent independently within their lifetime. The human dependence on cumulative culture may have shaped the evolution of biological and behavioral traits in the hominin lineage, including brain size, body size, life history, sociality, subsistence, and ecological niche expansion. Yet, we do not know when, in the human career, our ancestors began to depend on cumulative culture. Here, we show that hominins likely relied on a derived form of cumulative culture by at least ~600 kya, a result in line with a growing body of existing evidence. We analyzed the complexity of stone tool manufacturing sequences over the last 3.3 My of the archaeological record. We then compare these to the achievable complexity without cumulative culture, which we estimate using nonhuman primate technologies and stone tool manufacturing experiments. We find that archaeological technologies become significantly more complex than expected in the absence of cumulative culture only after ~600 kya.

Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.

The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin1. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts2, from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago3. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe4-6. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations7,8.

Late Middle Pleistocene Levallois stone-tool technology in southwest China.

Levallois approaches are one of the best known variants of prepared-core technologies, and are an important hallmark of stone technologies developed around 300,000 years ago in Africa and west Eurasia1,2. Existing archaeological evidence suggests that the stone technology of east Asian hominins lacked a Levallois component during the late Middle Pleistocene epoch and it is not until the Late Pleistocene (around 40,000-30,000 years ago) that this technology spread into east Asia in association with a dispersal of modern humans. Here we present evidence of Levallois technology from the lithic assemblage of the Guanyindong Cave site in southwest China, dated to approximately 170,000-80,000 years ago. To our knowledge, this is the earliest evidence of Levallois technology in east Asia. Our findings thus challenge the existing model of the origin and spread of Levallois technologies in east Asia and its links to a Late Pleistocene dispersal of modern humans.

Signatures of adaptive evolution in platyrrhine primate genomes.

The platyrrhine family Cebidae (capuchin and squirrel monkeys) exhibit among the largest primate encephalization quotients. Each cebid lineage is also characterized by notable lineage-specific traits, with capuchins showing striking similarities to Hominidae such as high sensorimotor intelligence with tool use, advanced cognitive abilities, and behavioral flexibility. Here, we take a comparative genomics approach, performing genome-wide tests for positive selection across five cebid branches, to gain insight into major periods of cebid adaptive evolution. We uncover candidate targets of selection across cebid evolutionary history that may underlie the emergence of lineage-specific traits. Our analyses highlight shifting and sustained selective pressures on genes related to brain development, longevity, reproduction, and morphology, including evidence for cumulative and diversifying neurobiological adaptations across cebid evolution. In addition to generating a high-quality reference genome assembly for robust capuchins, our results lend to a better understanding of the adaptive diversification of this distinctive primate clade.

Human Neuroimaging Reveals Differences in Activation and Connectivity between Real and Pantomimed Tool Use.

Because the sophistication of tool use is vastly enhanced in humans compared with other species, a rich understanding of its neural substrates requires neuroscientific experiments in humans. Although functional magnetic resonance imaging (fMRI) has enabled many studies of tool-related neural processing, surprisingly few studies have examined real tool use. Rather, because of the many constraints of fMRI, past research has typically used proxies such as pantomiming despite neuropsychological dissociations between pantomimed and real tool use. We compared univariate activation levels, multivariate activation patterns, and functional connectivity when participants used real tools (a plastic knife or fork) to act on a target object (scoring or poking a piece of putty) or pantomimed the same actions with similar movements and timing. During the Execute phase, we found higher activation for real versus pantomimed tool use in sensorimotor regions and the anterior supramarginal gyrus, and higher activation for pantomimed than real tool use in classic tool-selective areas. Although no regions showed significant differences in activation magnitude during the Plan phase, activation patterns differed between real versus pantomimed tool use and motor cortex showed differential functional connectivity. These results reflect important differences between real tool use, a closed-loop process constrained by real consequences, and pantomimed tool use, a symbolic gesture that requires conceptual knowledge of tools but with limited consequences. These results highlight the feasibility and added value of employing natural tool use tasks in functional imaging, inform neuropsychological dissociations, and advance our theoretical understanding of the neural substrates of natural tool use.SIGNIFICANCE STATEMENT The study of tool use offers unique insights into how the human brain synthesizes perceptual, cognitive, and sensorimotor functions to accomplish a goal. We suggest that the reliance on proxies, such as pantomiming, for real tool use has (1) overestimated the contribution of cognitive networks, because of the indirect, symbolic nature of pantomiming; and (2) underestimated the contribution of sensorimotor networks necessary for predicting and monitoring the consequences of real interactions between hand, tool, and the target object. These results enhance our theoretical understanding of the full range of human tool functions and inform our understanding of neuropsychological dissociations between real and pantomimed tool use.

MEvA-X: a hybrid multiobjective evolutionary tool using an XGBoost classifier for biomarkers discovery on biomedical datasets.

MOTIVATION: Biomarker discovery is one of the most frequent pursuits in bioinformatics and is crucial for precision medicine, disease prognosis, and drug discovery. A common challenge of biomarker discovery applications is the low ratio of samples over features for the selection of a reliable not-redundant subset of features, but despite the development of efficient tree-based classification methods, such as the extreme gradient boosting (XGBoost), this limitation is still relevant. Moreover, existing approaches for optimizing XGBoost do not deal effectively with the class imbalance nature of the biomarker discovery problems, and the presence of multiple conflicting objectives, since they focus on the training of a single-objective model. In the current work, we introduce MEvA-X, a novel hybrid ensemble for feature selection (FS) and classification, combining a niche-based multiobjective evolutionary algorithm (EA) with the XGBoost classifier. MEvA-X deploys a multiobjective EA to optimize the hyperparameters of the classifier and perform FS, identifying a set of Pareto-optimal solutions and optimizing multiple objectives, including classification and model simplicity metrics. RESULTS: The performance of the MEvA-X tool was benchmarked using one omics dataset coming from a microarray gene expression experiment, and one clinical questionnaire-based dataset combined with demographic information. MEvA-X tool outperformed the state-of-the-art methods in the balanced categorization of classes, creating multiple low-complexity models and identifying important nonredundant biomarkers. The best-performing run of MEvA-X for the prediction of weight loss using gene expression data yields a small set of blood circulatory markers which are sufficient for this precision nutrition application but need further validation. AVAILABILITY AND IMPLEMENTATION: https://github.com/PanKonstantinos/MEvA-X.

Relationship Between Patient Portal Tool Use and Medication Adherence and Viral Load Among Patients Living with HIV.

BACKGROUND: Patient portals play an increasingly critical role in engaging patients in their health care. They have the potential to significantly impact the health of those living with chronic diseases, such as HIV, for whom consistent care engagement is both critical and complex. OBJECTIVE: The primary aim was to examine the longitudinal relationships between individual portal tool use and health-related outcomes in patients living with HIV. DESIGN: Retrospective cohort study using electronic health record data to examine the relationship between patient portal tool use and key HIV-specific, health-related outcomes in patients engaged in care in the Veterans Health Administration (VA) through the application of marginal structural models. PARTICIPANTS: A national sample of patients living with HIV (PLWH) active in VA care who were registered to use the VA's patient portal, My HealtheVet (MHV; n = 18,390) between 10/1/2012 and 4/1/2017. MAIN MEASURES: The MHV tools examined were prescription refill (including prescription refill of an antiretroviral (ART) medication and any medication), secure messaging, view appointments, and view labs. Primary outcomes were viral load test receipt, viral load suppression, and ART medication adherence (measured as proportion of days covered). KEY RESULTS: The use of prescription refill for any medication or for ART was positively associated with ART adherence. Secure messaging was positively associated with ART adherence but not with viral load test receipt or viral load suppression. The use of view appointments was positively associated with ART adherence and viral load test receipt but not viral load suppression. The use of view labs was positively associated with viral load suppression but not ART adherence or viral load test receipt. CONCLUSIONS: These findings highlight the valuable role patient portals may play in improving health-related outcomes among PLWH and have implications for patients living with other types of chronic disease.

The archaeological visibility of chimpanzee (Pan troglodytes) nut-cracking.

The earliest evidence for complex tool use in the archaeological record dates to 3.3 Ma. While wooden tools may have been used by our earliest ancestors, the evidence is absent due to poor preservation. However, insights into possible early hominin wooden tool use can be gained from observing the tool-use practices of our closest living relatives, chimpanzees (Pan troglodytes). By using stone hammers used to crack various nuts, chimpanzees leave a durable material signature comprised of formal tools and associated diagnostic fragments. While the archaeological evidence of chimpanzee wooden tool use is temporary, the combination of stone hammers and wooden anvils can create a more enduring lithic record. This study explores the lithic assemblages associated with wooden and stone anvil use at nut-cracking sites in Taï National Park, Côte d'Ivoire, using technological and use-wear analyses. Our results indicate clear differences in density, fracture patterns, and use-wear in the lithic records between wooden anvil and stone anvil sites. New archaeological excavations at six chimpanzee nut-cracking sites reveal that the anvils' material directly influences the visibility of nut-cracking evidence in the archaeological record. By examining the nature of the lithic signatures associated with wooden anvil and stone anvil use by chimpanzees, we can formulate hypotheses about the probability of such behaviors being preserved and identifiable in the Plio-Pleistocene hominin archaeological record. The variability in material signatures from nut-cracking on different anvils suggests that stone anvils leave a clear archaeological record. Evidence for wooden anvil use is likely underrepresented due to the more ephemeral nature of the associated percussive damage and material signature. It may, however, still be possible, albeit challenging, to identify wooden anvil use in the archaeological record.

Hooded crows (Corvus cornix) manufacture objects relative to a mental template.

It was recently found that not only tool-specialized New Caledonian crows, but also Goffin cockatoos can manufacture physical objects in accordance with a mental template. That is, they can emulate features of existing objects when they manufacture new items. Both species spontaneously ripped pieces of card into large strips if they had previously learned that a large template was rewarded, and small strips when they previously learned that a small template was rewarded. Among New Caledonian crows, this cognitive ability was suggested as a potential mechanism underlying the transmission of natural tool designs. Here, we tested for the same ability in another non-specialised tool user-Hooded crows (Corvus cornix). Crows were exposed to pre-made template objects, varying first in colour and then in size, and were rewarded only if they chose pre-made objects that matched the template. In subsequent tests, birds were given the opportunity to manufacture versions of these objects. All three crows ripped paper pieces from the same colour material as the rewarded template, and, crucially, also manufactured objects that were more similar in size to previously rewarded, than unrewarded, templates, despite the birds being rewarded at random in both tests. Therefore, we found the ability to manufacture physical objects relative to a mental template in yet another bird species not specialized in using or making foraging tools in the wild, but with a high level of brain and cognitive development.

Proto-tool use for food processing in wild Arabian babblers: matching processing methods, substrates and prey types.

Cognition is a powerful adaptation, enabling animals to utilise resources that are unavailable without manipulation. Tool use and food processing are examples of using cognition to overcome the protective mechanisms of food resources. Here, we describe and examine the flexibility of proto-tool use (defined as the alteration of an object through object-substrate manipulation) for food processing in a cooperatively breeding bird, the Arabian babbler (Argya squamiceps). Field observations demonstrate that the birds transport different caterpillar species to different substrate types depending on the processing method needed to prepare the caterpillar for eating. Species with toxic setae (e.g. Casama innotata) are transported to be rubbed on rough substrates (e.g. sand) before consumption, while other species (e.g. Hyles livornica) are transported to be pounded against hard substrates until their inner organs are removed and only their external body part is consumed. These results are among the few to describe flexible proto-tool use for food processing in wild animals. They thereby contribute to the taxonomic mapping of proto-tool use and food processing in non-human species, which is a fundamental step to advance comparative studies on the evolution of these behaviours and their underlying cognitive mechanisms.

The Determination of Diabetes Utilities, Costs, and Effects Model: A Cost-Utility Tool Using Patient-Level Microsimulation to Evaluate Sensor-Based Glucose Monitoring Systems in Type 1 and Type 2 Diabetes: Comparative Validation.

OBJECTIVES: To assess the accuracy and validity of the Determination of Diabetes Utilities, Costs, and Effects (DEDUCE) model, a Microsoft-Excel-based tool for evaluating diabetes interventions for type 1 and type 2 diabetes. METHODS: The DEDUCE model is a patient-level microsimulation, with complications predicted based on the Sheffield and Risk Equations for Complications Of type 2 diabetes models for type 1 and type 2 diabetes, respectively. For this tool to be useful, it must be validated to ensure that its complication predictions are accurate. Internal, external, and cross-validation was assessed by populating the DEDUCE model with the baseline characteristics and treatment effects reported in clinical trials used in the Fourth, Fifth, and Ninth Mount Hood Diabetes Challenges. Results from the DEDUCE model were evaluated against clinical results and previously validated models via mean absolute percentage error or percentage error. RESULTS: The DEDUCE model performed favorably, predicting key outcomes, including cardiovascular disease in type 1 diabetes and all-cause mortality in type 2 diabetes. The model performed well against other models. In the Mount Hood 9 Challenge comparison, error was below the mean reported from comparator models for several outcomes, particularly for hazard ratios. CONCLUSIONS: The DEDUCE model predicts diabetes-related complications from trials and studies well when compared with previously validated models. The model may serve as a useful tool for evaluating the cost-effectiveness of diabetes technologies.

An empirical comparison of statistical methods for multiple cut-off diagnostic test accuracy meta-analysis of the Edinburgh postnatal depression scale (EPDS) depression screening tool using published results vs individual participant data.

BACKGROUND: Selective reporting of results from only well-performing cut-offs leads to biased estimates of accuracy in primary studies of questionnaire-based screening tools and in meta-analyses that synthesize results. Individual participant data meta-analysis (IPDMA) of sensitivity and specificity at each cut-off via bivariate random-effects models (BREMs) can overcome this problem. However, IPDMA is laborious and depends on the ability to successfully obtain primary datasets, and BREMs ignore the correlation between cut-offs within primary studies. METHODS: We compared the performance of three recent multiple cut-off models developed by Steinhauser et al., Jones et al., and Hoyer and Kuss, that account for missing cut-offs when meta-analyzing diagnostic accuracy studies with multiple cut-offs, to BREMs fitted at each cut-off. We used data from 22 studies of the accuracy of the Edinburgh Postnatal Depression Scale (EPDS; 4475 participants, 758 major depression cases). We fitted each of the three multiple cut-off models and BREMs to a dataset with results from only published cut-offs from each study (published data) and an IPD dataset with results for all cut-offs (full IPD data). We estimated pooled sensitivity and specificity with 95% confidence intervals (CIs) for each cut-off and the area under the curve. RESULTS: Compared to the BREMs fitted to the full IPD data, the Steinhauser et al., Jones et al., and Hoyer and Kuss models fitted to the published data produced similar receiver operating characteristic curves; though, the Hoyer and Kuss model had lower area under the curve, mainly due to estimating slightly lower sensitivity at lower cut-offs. When fitting the three multiple cut-off models to the full IPD data, a similar pattern of results was observed. Importantly, all models had similar 95% CIs for sensitivity and specificity, and the CI width increased with cut-off levels for sensitivity and decreased with an increasing cut-off for specificity, even the BREMs which treat each cut-off separately. CONCLUSIONS: Multiple cut-off models appear to be the favorable methods when only published data are available. While collecting IPD is expensive and time consuming, IPD can facilitate subgroup analyses that cannot be conducted with published data only.

MLDSPP: Bacterial Promoter Prediction Tool Using DNA Structural Properties with Machine Learning and Explainable AI.

Bacterial promoters play a crucial role in gene expression by serving as docking sites for the transcription initiation machinery. However, accurately identifying promoter regions in bacterial genomes remains a challenge due to their diverse architecture and variations. In this study, we propose MLDSPP (Machine Learning and Duplex Stability based Promoter prediction in Prokaryotes), a machine learning-based promoter prediction tool, to comprehensively screen bacterial promoter regions in 12 diverse genomes. We leveraged biologically relevant and informative DNA structural properties, such as DNA duplex stability and base stacking, and state-of-the-art machine learning (ML) strategies to gain insights into promoter characteristics. We evaluated several machine learning models, including Support Vector Machines, Random Forests, and XGBoost, and assessed their performance using accuracy, precision, recall, specificity, F1 score, and MCC metrics. Our findings reveal that XGBoost outperformed other models and current state-of-the-art promoter prediction tools, namely Sigma70pred and iPromoter2L, achieving F1-scores >95% in most systems. Significantly, the use of one-hot encoding for representing nucleotide sequences complements these structural features, enhancing our XGBoost model's predictive capabilities. To address the challenge of model interpretability, we incorporated explainable AI techniques using Shapley values. This enhancement allows for a better understanding and interpretation of the predictions of our model. In conclusion, our study presents MLDSPP as a novel, generic tool for predicting promoter regions in bacteria, utilizing original downstream sequences as nonpromoter controls. This tool has the potential to significantly advance the field of bacterial genomics and contribute to our understanding of gene regulation in diverse bacterial systems.

Earliest known hominin activity in the Philippines by 709 thousand years ago.

Over 60 years ago, stone tools and remains of megafauna were discovered on the Southeast Asian islands of Flores, Sulawesi and Luzon, and a Middle Pleistocene colonization by Homo erectus was initially proposed to have occurred on these islands1-4. However, until the discovery of Homo floresiensis in 2003, claims of the presence of archaic hominins on Wallacean islands were hypothetical owing to the absence of in situ fossils and/or stone artefacts that were excavated from well-documented stratigraphic contexts, or because secure numerical dating methods of these sites were lacking. As a consequence, these claims were generally treated with scepticism 5 . Here we describe the results of recent excavations at Kalinga in the Cagayan Valley of northern Luzon in the Philippines that have yielded 57 stone tools associated with an almost-complete disarticulated skeleton of Rhinoceros philippinensis, which shows clear signs of butchery, together with other fossil fauna remains attributed to stegodon, Philippine brown deer, freshwater turtle and monitor lizard. All finds originate from a clay-rich bone bed that was dated to between 777 and 631 thousand years ago using electron-spin resonance methods that were applied to tooth enamel and fluvial quartz. This evidence pushes back the proven period of colonization 6 of the Philippines by hundreds of thousands of years, and furthermore suggests that early overseas dispersal in Island South East Asia by premodern hominins took place several times during the Early and Middle Pleistocene stages1-4. The Philippines therefore may have had a central role in southward movements into Wallacea, not only of Pleistocene megafauna 7 , but also of archaic hominins.