bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing machine learning to boost heuristic strategies for phylogenetic-tree search
Authors: Azouri Dana , Abadi Shiran , Mansour Yishay , Mayrose Itay , Pupko Tal 
Published: August 2020

Abstract
Inferring a phylogenetic tree, which describes the evolutionary relationships among a set of organisms, genes, or genomes, is a fundamental step in numerous evolutionary studies. With the aim of making tree inference feasible for problems involving more than a handful of sequences, current algorithms for phylogenetic tree reconstruction utilize various heuristic approaches. Such approaches rely on performing costly likelihood optimizations, and thus evaluate only a subset of all potential trees. Consequently, all existing methods suffer from the known tradeoff between accuracy and running time. Here, we train a machine-learning algorithm over an extensive cohort of empirical data to predict the neighboring trees that increase the likelihood, without actually computing their likelihood. This provides means to safely discard a large set of the search space, thus avoiding numerous expensive likelihood computations. Our analyses suggest that machine-learning approaches can make heuristic tree searches substantially faster without losing accuracy and thus could be incorporated for narrowing down the examined neighboring trees of each intermediate tree in any tree search methodology.
Hominin Ecology of the Early Oldowan 2 Ma
Authors: Mercader Julio , Akuku Pamela , Boivin Nicole , Bugumba Revocatus , Bushozi Pastory , Camacho Alfredo , Carter Tristan , Clarke Siobhán , Cueva-Temprana Arturo , Durkin Paul , Favreau Julien , Fella Kelvin , Haberle Simon , Hubbard Stephen , Inwood Jamie , Itambu Makarius , Koromo Samson , Lee Patrick , Mohammed Abdallah , Mwambwiga Aloyce , Olesilau Lucas , Patalano Robert , Roberts Patrick , Rule Susan , Saladie Palmira , Siljedal Gunnar , Soto María , Umbsaar Jonathan , Petraglia Michael 
Published: August 2020

Abstract
Environmental change is key for human evolution, especially at times of anatomical and behavioral change in life histories, such as the origin of meat consumption, economic diversification, and dispersal. However, for the earliest phase of human evolution featuring the technology-dependent hominins that shaped our lineage since 2.6 Ma, the Oldowan, there is a dearth of archaeological evidence directly associated with rich chronostratigraphic and environmental datasets amenable to tracking ecological change and adaptation to new physiographic conditions. One place where this type of information has been recently retrieved is the Western Plio-Pleistocene rift basin of Olduvai Gorge (now Oldupai), Tanzania. We explore habitat range by Oldowan-bearing hominins amidst extremely diverse ecosystems throughout a stratified sequence 235 ka-long, thus predating by >180 ka the earliest landmark fossil hominins and classic Oldowan from the Eastern side of the basin. Our study provides multi-proxy evidence of environmental adaptability, demonstrating colonisation of fresh volcanic landscapes and occupation of fast-changing biomes by 2 Ma.
Three Thousand Year Paleotsunami History of Southern Part of Japan Trench
Authors: Higaki Hokuto , Goto Kazuhisa , Yanagisawa Hideaki , Sugawara Daisuke , Ishizawa Takashi 
Published: August 2020

Abstract
Paleotsunami studies along the southern part of Japan Trench are scarce. Additional geological evidence must be collected. This study conducted field survey and multi-proxy analysis for drilling cores taken from a pond of Choshi City, Chiba prefecture, Japan, where the 1677 Enpo tsunami deposit was reported earlier. The pond is suitable for detection of sedimentary evidence of low-frequency but large tsunamis only because it is located at a high elevation (11 m). Three event deposits are intercalated in the three thousand year long continuous mud and peat sequences. Based on multi-proxy analyses conducted of grain size distributions, diatom assemblages, and geochemical markers, these event deposits were identified as tsunami deposits; the most recent was the AD 1677 Enpo tsunami. The estimated recurrence interval of the tsunami is approximately 700 years, which is comparable to those of the central part of the Japan Trench. It is noteworthy that the timing of these tsunami events along the southern part of the Japan Trench seems to have been close (few tens of years intervals) before or after the occurrence of large earthquakes and tsunamis along the central part of the Japan Trench. Therefore, a spatial-temporal relation of earthquake and tsunami generations might exist between central and southern parts of the Japan Trench, which might be explained by drastic changes of stress fields surrounding the rupture area of a huge earthquake. Considering the current situation, by which the Mw=9.0 2011 Tohoku-oki earthquake had occurred at central part of the Japan Trench, this possibility should be investigated carefully from perspectives of seismology and history because risks of future occurrence of large earthquake and tsunami events along the southern part of Japan Trench might be extremely high.
Comparing Cost and Print Time Estimates for Six Commercially-Available 3D Printers Obtained Through Slicing Software for Clinically Relevant Anatomical Models
Authors: Chen Joshua Vic , Dang Alan BC , Dang Alexis 
Published: August 2020

Abstract
Background3D printed patient-specific anatomical models have been applied clinically to orthopaedic care for surgical planning and patient education. The estimated cost and print time per model for 3D printers have not yet been compared with clinically representative models across multiple printing technologies. This study investigates six commercially available 3D printers: Prusa i3 MK3S, Formlabs Form 2, Formlabs Form 3, LulzBot TAZ 6, Stratasys F370, and Stratasys J750 Digital Anatomy.MethodsSeven representative orthopaedic standard tessellation models derived from anonymized CT scans were imported into the respective slicing software for each 3D printer. For each 3D printer and corresponding print setting, the slicing software provides a computed print time and material use estimate. Material quantity was used to calculate estimated model cost. Print settings investigated were infill percentage, layer height, and model orientation on the print bed. The slicing software investigated are Cura LulzBot Edition 3.6.20, GrabCAD Print 1.43, PreForm 3.4.6, and PrusaSlicer 2.2.0.ResultsThe effect of changing infill between 15% and 20% on estimated print time and material use appears to be negligible. Orientation of the model has considerable impact on time and cost with worst-case differences being as much as 39.30% added print time and 34.56% added costs. Averaged across all investigated settings, horizontal model orientation on the print bed minimizes estimated print time for all 3D printers, while vertical model orientation generally minimizes cost with the exception of Stratasys J750 Digital Anatomy, in which horizontal model orientation also minimized cost. Decreasing layer height for all investigated 3D printers increased estimated print time and decreased estimated cost with the exception of Stratasys F370, in which cost increased. The difference in material cost was approximately two orders of magnitude between the least and most-expensive printers.ConclusionsAll investigated 3D printers in this study have the potential for clinical utility. Print time and print cost are dependent on orientation of anatomy and the 3D printers and settings selected. Cost-effective clinical 3D printing of anatomic models should consider an appropriate printer for the complexity of the anatomy and the experience of the printer technicians.
Rapid endogenic rock recycling in magmatic arcs
Authors: Li Junyong , Tang Ming , Lee Cin-Ty , Wang Xiaolei , Gu Zhi-Dong , Xia Xiao-Ping , Wang Di , Du De-Hong , Li Lin-Sen 
Published: August 2020

Abstract
In subduction zones, materials on Earth’s surface can be transported to the deep crust or mantle, but the exact mechanisms and the nature of the recycled materials are not fully understood. Here, we report a set of migmatites from western Yangtze Block, China. These migmatites have similar bulk compositions as forearc sediments. Zircon age distribution and Hf–O isotopes indicate that the precursors of the sediments were predominantly derived from juvenile arc crust itself. Using phase equilibria modelling, we show that the sediments experienced high temperature-to-pressure ratio metamorphism and were most likely transported to deep arc crust by intracrustal thrust faults. By dating the magmatic zircon cores and overgrowth rims, we find that the entire rock cycle, from arc magmatism, to weathering at the surface, then to burial and remelting in the deep crust, took place within ~ 10 Ma. Our findings highlight thrust faults as an efficient recycling channel in compressional arcs and endogenic recycling as an important mechanism driving internal redistribution and differentiation of arc crust.
Forever young white dwarfs: when stellar ageing stops
Authors: Camisassa Maria , Althaus Leandro , Torres Santiago , Córsico Alejandro , Cheng Sihao , Rebassa-Mansergas Alberto 
Published: August 2020

Abstract
White dwarf stars are the most common end point of stellar evolution. In particular, ultra-massive white dwarfs are expected to harbour oxygen-neon (ONe) cores as a result of single standard stellar evolution. However, a fraction of them could have carbon-oxygen (CO) cores and be born as a result of merger events. Recent observations provided by Gaia space mission, indicate that a fraction of the ultra-massive white dwarfs experience a strong delay in their cooling, which cannot be attributed only to the occurrence of crystallization, thus requiring an unknown energy source able to prolong their life for long periods of time. Here, we show that the energy released by 22Ne sedimentation in ultra-massive white dwarfs with CO cores is at the root of the long cooling delay of these stars. Our results provide solid sustain to the existence of CO-core ultra-massive white dwarfs and the occurrence of stellar mergers.
Transforaminal Epidural Steroid Injection Combined with Radio Frequency for the Treatment of Lumbar Disc Herniation: A 2-year Follow-up
Authors: Wei Wenbo , Dang Shajie , Wei Ling , Liu Tian , Wang Jue 
Published: August 2020

Abstract
Objective: To assess the therapeutic efficacy of transforaminal epidural steroid injection (TFESI) combined with radio frequency (RF) for the treatment of lumbar disc herniation (LDH). Methods: A total of 230 patients participated in the study: TFESI (Group T, n=110), TFESI combined with RF (Group TR, n=120). Visual analogue scale (VAS), Oswestry disability index (ODI) and Global perceived effect (GPE) scale were measured pre-operation, 1, 3, 6, 12 and 24 months after the operation. Hospitalization time, operation time, complications, and recurrence were compared between the two groups.Results: The VAS and ODI at each observation point of the post-operation were significantly decreased compared with the pre-operation in both groups (P < 0.05). There was no statistically different of VAS and ODI between the two groups at 1 and 3 months of the post-operation (P > 0.05). However, The VAS and ODI scores in Group TR were significantly lower than that in Group T at 6, 12 and 24 months of the post-operation (P < 0.05). The GPE in group TR was high in the early days, while that at 1 and 3 month after treatment was significantly higher than that in group T (P < 0.05). The recurrence rate in Group TR was lower than that in Group T (P = 0.002). There was no significant difference of hospitalization time, complications, VAS and ODI score at the pre-operation between the two groups (P > 0.05).Conclusion: These findings suggest that TFESI combined with RF could effectively improve the pain and function, and had a long-term satisfactory effect for the treatment of LDH.
Elevated oxygen demand in a case of COVID-19 with severe ARDS: a point for optimal oxygenation therapy including ECMO management
Authors: Oshima Taku , Oami Takehiko , Yamashiro Mana , Higashi Akiko , Hayashi Yosuke , Suga Natsumi , Takayanagi Shin , Sakao Seiichiro , Nakada Taka-aki 
Published: August 2020

Abstract
Background: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become a global pandemic, and those developing critically ill conditions have been reported to have mortality in the range of 39% to 61%. Due to the lack of definitive treatments, mechanical ventilation and supportive oxygenation therapy are key management strategies for the survival of patients with acute respiratory distress syndrome (ARDS). Optimizing oxygenation therapy is mandatory to treat patients with severe respiratory failure, to sufficiently compensate for the oxygen (O2) demand. We experienced a case of severe ARDS due to COVID-19 successfully treated with extracorporeal membrane oxygenation (ECMO) after increasing oxygen delivery according to O2 consumption measurement by indirect calorimetryCase Presentation: A 29-year-old obese but otherwise healthy man was hospitalized for treatment of COVID-19 pneumonia presenting with a 4-day history of persisting cough, high fever, and dyspnea. Mechanical ventilation, nitric oxide inhalation, and prone positioning were initiated in the ICU against severe respiratory dysfunction. Indirect calorimetry on the 3rd and 6th ICU days revealed persistent elevation of oxygen consumption (VO2) of 380 mL/min. Veno-venous ECMO was initiated on the 7th ICU day after further deterioration of respiratory failure. Periodic events of SpO2 decline due to effortful breathing was not resolved by neuromuscular blockade in attempt to reduce O2 consumption. Increasing the ECMO flow induced hemolysis and hyperkalemia despite the use of large bore cannulas and ECMO circuit free of clots and defects. The hemoglobin management level was elevated from 10 g/dL to 13 g/dL to increase blood oxygen capacity, enabling the reduction of ECMO flow while attenuating respiratory effort and maintaining SpO2. Lung protective ventilation strategy and prone positioning were continued for successful weaning from ECMO on the 16th ICU day, and the ventilator on the 18th ICU day.Conclusion: The present case of severe ARDS due to COVID-19 was successfully treated with ECMO. Enhancing oxygen delivery was crucial to compensate for the elevated O2 demand. Measuring O2 consumption by indirect calorimetry can elucidate the oxygen demand for optimizing the oxygenation therapy for successful management and survival of critically ill COVID-19 patients.
How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology
Authors: Casey William , Massey Steven , Mishra Bud 
Published: August 2020

Abstract
Mimicry is exhibited in multiple scales, ranging from molecular, to organismal, and then to human society. ‘Batesian’ type mimicry entails a conflict of interest between sender and receiver, reflected in a deceptive mimic signal. ‘Mullerian’ type mimicry occurs when there is perfect common interest between sender and receiver, manifested by an honest co-mimic signal. Using a signaling games approach, simulations show that invasion by Batesian mimics will make Mullerian mimicry unstable, in a coevolutionary chase. We use these results to better understand the deceptive strategies of SARS-CoV-2 and their key role in the COVID-19 pandemic. At the biomolecular level, we explain how cellularization promotes Mullerian molecular mimicry, and discourages Batesian molecular mimicry. A wide range of processes analogous to cellularization are presented; these might represent a manner of reducing oscillatory instabilities. Lastly, we identify examples of mimicry in human society, that might be addressed using a signaling game approach.
Vision 2030 and Sustainable Development: State Capacity to Revitalize the Healthcare System in Saudi Arabia
Authors: Rahman Redwan , Qattan Ameerah 
Published: August 2020

Abstract
Vision 2030 is seen as a contributing factor to diversifying the Kingdom of Saudi Arabia’s economy and stimulating numerous changes in its social sectors, including in the health sector. Sustainable Development (SD)2030 is a global consensual agreement among nation states to build a sustainable, desirable and progressively interrelated world. Achieving the Sustainable Development 2030 is seen as a main component of development for health. This article explores the state capacity and the role of Vision2030 and Sustainable Development 2030 in the revitalizing the healthcare system in Saudi Arabia. Systematic review and thematic data analysis technique are used as method of this study. The Saudi government highlighted and emphasized Vision 2030 to improve population health and the world body emphasized that Sustainable Development 2030 will contribute to “healthy lives and promote well-being for all at all ages”. Saudi Arabia’s Vision2030 encourages the state to play a renewed role in development in the light of the UN’s declaration of the ‘right to development’. In pursuing development, the state must have necessary institutional environment in sustaining capacity, resources and interactions among groups for realizing constructive roles and functions in maintaining state affairs. The government needs to develop a sustainable healthcare system by adding to health human resources, building public-private partnership, and efficient use of resources through stewardship, good governance, accountability, and transparency.
An Automated Workflow to Screen Alkene Reductases Using High-throughput Thin Layer Chromatography
Authors: Garabedian Brett M. , Meadows Corey W. , Mingardon Florence , Guenther Joel M. , de Rond Tristan , Abourjeily Raya , Lee Taek Soon 
Published: August 2020

Abstract
Background: Synthetic biology efforts often require high-throughput screening tools for enzyme engineering campaigns. While innovations in chromatographic and mass spectrometry-based techniques provide relevant structural information associated with enzyme activity, these approaches can require cost-intensive instrumentation and technical expertise not broadly available. Moreover, complex workflows and analysis time can significantly impact throughput. To this end, we develop an automated, 96-well screening platform based on thin layer chromatography (TLC) and use it to monitor in vitro activity of a geranylgeranyl reductase isolated from Sulfolobus acidocaldarius (SaGGR). Results: Unreduced SaGGR products are oxidized to their corresponding epoxide and applied to thin layer silica plates by acoustic printing. These derivatives are chromatographically separated based on the number of epoxides they possess and are covalently ligated to a chromophore, allowing detection of enzyme variants with unique product distributions or enhanced reductase activity. Herein, we employ this workflow to examine farnesol reduction using a codon-saturation mutagenesis library at site Leu377 of SaGGR. We show this TLC-based screen can distinguish between 4-fold differences in enzyme activity for select mutants and validated those results by GC-MS. Conclusions: With appropriate quantitation methods, this workflow can be used to screen polyprenyl reductase activity and can be readily adapted to analyze broader catalyst libraries whose products are amenable to TLC analysis.
Host genetics affected the resistome and its expression patterns in the rumen of beef cattle raised without antibiotics used in humans
Authors: Ma Tao , Li Fuyong , Zaheer Rahat , McAllister Tim A. , Guan Le Luo 
Published: August 2020

Abstract
Background: The rumen microbiome is a potential reservoir of antimicrobial-resistant genes (ARGs), termly resistome. However, the activity of ARGs and what factors affect expression of ARGs in the rumen is unknown. Here, the rumen resistome was evaluated using metagenomic and metatranscriptomic datasets, with the aim to identify the active rumen resistome and whether it can be affected by cattle breed and feed efficiency.Results: Genes encoding resistance to 12 ARG classes representing 62 individual ARGs were detected in the rumen metagenomes of Angus, Charolais or Kinsella composite hybrid (KC) beef steers (n = 48) with high and low feed efficiency. Three genes encoding tetracycline (tetQ, tetW) and macrolide (mefA) resistance constituted 75.3% of abundance of total ARGs identified in all animals, suggesting they are ‘core’ resistome in the rumen of steers. Only about 20.96% (13/62) of the total ARGs identified were expressed, among which genes encoding resistance to tetracycline, macrolide-licosamide-streptogramin (MLS), aminoglycoside, and multidrug exhibited the highest level of expression. More than half (56.2%) of the ARGs identified were plasmid-associated, while only 5 plasmid-associated ARGs were expressed. The abundance of 17, 14, and 5 individual ARGs were significantly affected by breed, feed efficiency, and breed × feed efficiency, respectively, while the expression of ARGs did not differ among breeds or between feed efficiency groups. In KC cattle, less number of total ARGs, ARG transcripts, as well as total active bacteria (estimated by 16S rRNA copies) was observed than AN. The total active bacteria were negatively correlated with expression of MLS and tetracycline ARG (mefA, tet40, tetM, tetW, and an unidentified tet), and tended to be negatively correlated with the expression of plasmid-associated tetracycline ARG t only in the rumen of KC cattle.Conclusions: Our results suggest that a large portion of the ARGs are not expressed in the rumen of cattle raised without antibiotics used in humans. The identified less diversified active resistome and total active bacteria, and the significant correlation between total active bacteria and the abundance of ARG transcripts in KC cattle suggest that the expression of resistome in the rumen may be breed specific and driven by ruminal microbiota.
Neonatal&nbsp;Oculocutaneous Albinism Type 2 With Prader-Willi Syndrome
Authors: Wu Gaohong , Yan Dongya , Zhou Meijuan , Li Wenmei , Jiang Ping , Zhu Xueping 
Published: August 2020

Abstract
Background: To investigate the pathogenesis and clinical characteristics of Oculocutaneous albinism type 2 (OCA2), a genetic condition in the etiology of Prader-Willi syndrome (PWS).Case presentation: A retrospective study of one case presented with poor response to stimuli, difficultfeeding, poor crying, with yellow hair and white skin. We performed genetic testing and investigated disease pathogenesis, clinical manifestations, and diagnosis, and discussed the characteristics of the disease through a literature review. HiSeq high-throughput sequencing result suggested a deletion with 105 genes, including UBE3A, SNRPN, OCA2, and other genes up to 5.18 Mb on the long arm of chromosome (15q11-13 region), a critical region, susceptible to the PWS. A paternally derived deletion Del (15q11. 2q13. 1) [GRCh37 / hg19] (23, 378, 392-28, 563, 050) × 1, and a maternal missense mutation were identified in the OCA2 gene (chr15: 28171296 c .2056G> A (p.A686T). During the period of hospitalization, the child still suffered from poor milk intake, and she was discharged from the hospital at the request of her parents. After discharge, the patient was followed up for two months by telephone. However, the patient died of feeding difficulties and pulmonary infection.Conclusions: OCA2 combined with PWS due to OCA2 gene missense mutation combined with large fragment deletion of 15q11-13 region was first reported in this study, of which the clinical signs can be subtle and symptoms can be more severe, therefore, early genetic testing is crucial for those patients to yield an accurate diagnosis and initiate aggressive interventions to optimize the outcomes.