bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow
Authors: Jiao Xiyun , Flouri Tomáš , Yang Ziheng 
Published: July 2021

AbstractMultispecies coalescent (MSC) is the extension of the single-population coalescent model to multiple species. It integrates the phylogenetic process of species divergences and the population genetic process of coalescent, and provides a powerful framework for a number of inference problems using genomic sequence data from multiple species, including estimation of species divergence times and population sizes, estimation of species trees accommodating discordant gene trees, inference of cross-species gene flow and species delimitation. In this review, we introduce the major features of the MSC model, discuss full-likelihood and heuristic methods of species tree estimation and summarize recent methodological advances in inference of cross-species gene flow. We discuss the statistical and computational challenges in the field and research directions where breakthroughs may be likely in the next few years.
Highest-resolution rotation curve of the inner Milky Way proving the galactic shock wave
Authors: Sofue Yoshiaki 
Published: July 2021

Abstract
We present a rotation curve (RC) of the inner Galaxy of the first quadrant at 10° ≤ l ≤ 50° (R = 1.3–6.2 kpc) with the highest spatial (2 pc) and velocity (1.3 km s−1) resolutions. We used 12CO(J = 1–0)-line survey data observed with the Nobeyama 45 m telescope at an effective angular resolution of 20″ (originally 15″), and applied the tangent–velocity method to the longitude–velocity diagrams by employing the Gaussian deconvolution of the individual CO-line profiles. A number of RC bumps, or local variation of rotation velocity, with velocity amplitudes ∼±9 km s−1 and radial scale length ∼0.5–1 kpc are superposed on the mean rotation velocity. The prominent velocity bump and corresponding density variation around R ∼ 4 kpc in the tangential direction of the Scutum arm (4 kpc molecular arm) is naturally explained by an ordinary galactic shock wave in a spiral arm with small pitch angle, not necessarily requiring a bar-induced strong shock.
Subnational Politics and Redistribution in a Federal System: Determinants of Progressive Social Spending in Brazilian States
Authors: Dunn Claire 
Published: July 2021

AbstractWhat role do subnational governments play in shaping a country’s redistributive efforts? Existing literature suggests that federalism can be a hindrance to redistribution. Such negative effects may be particularly true of Latin America’s federations due to high levels of regional inequality and malapportioned political institutions. However, in order to fully understand redistribution in federal systems in Latin America, we need to examine not only how subnational governments affect centralized redistributive efforts, but also what efforts these subnational governments are making themselves. In this article, I contribute to our understanding of subnational social spending in Latin America’s largest federation, Brazil. My results suggest that, in Brazil, state governments are constrained actors, but they do pursue different levels of redistributive social spending with higher levels being more likely under left parties.
The well-being and the will of the people amid COVID-19
Authors: Rosales Renniel Jayson Jacinto , Adia Crizlene Magpantay , Miral Kiara Cristine Macuha 
Published: July 2021

Abstract
The well-being and the will of the Filipino people are now to be considered. With many people gathering and having leisure time, the well-being of the people is being balanced now. The spiritual, mental and social well-being of the people are being satisfied but with the consequence of putting our safety at stake because of the seemingly unending threat of the COVID-19 pandemic in the Philippines. We know that we want a normal life, but it seems too much for the people to stay at home while seeing other countries enjoy a post-pandemic life.
Enemies of the future? Questioning the regimes of promising in emerging science and technology
Authors: Robinson Douglas K R , Audétat Marc , Joly Pierre-Benoit , Van Lente Harro 
Published: July 2021

Abstract
This editorial introduces the basic idea and content of the special section ‘Enemies of the future? Questioning the regimes of promising in emerging science and technology’. It sheds light on how visions and stories of technological futures are being produced and, in combination, have stabilized into ‘regimes of promising’ that shape emerging technoscientific domains and guide research, innovation, and governance within these domains. The special section zooms in to particular illustrative instances that reveal the dynamics of the dominant regime of promising and also reveal how they are breaking down and in some cases being replaced by alternatives. The purpose of this special section is to show the importance of regimes of promising for research and innovation policy and to stimulate further discussions on alternative regimes of promising and their ramifications.
Effects of grain adaptation programs and antimicrobial feed additives on performance and nutrient digestibility of Bos indicus cattle fed whole shelled corn
Authors: Mobiglia Andrea M , Camilo Fernando R , Couto Victor R M , Castro Flavio G F , Drouillard James S , Gouvêa Vinícius N , Fernandes Juliano J R 
Published: July 2021

Abstract
Two experiments were conducted to evaluate the effects of feed additives [monensin (MON); 30 mg/kg of dry matter (DM), and virginiamycin (VM); 25 mg/kg DM] and grain adaptation programs [adding roughage (ROU; sugarcane bagasse) or not (NO-ROU) during the 20-d adaptation period] on performance, carcass characteristics, and nutrient digestibility of Bos indicus cattle fed finishing diets containing 85% whole shelled corn and 15% of a pelleted protein-mineral-vitamin supplement. In Exp.1, 105 Nellore bulls [initial body weight (BW) = 368 ± 25 kg] were used in a complete randomized block design with a 2 × 2 factorial arrangement of treatments, consisting of two feed additives (MON and VM) associated with two adaptation programs (ROU or NO-ROU during the 20-d adaptation period). Effects of feed additives × adaptation programs were not detected (P ≥ 0.13). Feed additives did not affect dry matter intake (DMI), average daily gain (ADG), and feed efficiency (G:F) during the 20-d adaptation period (P ≥ 0.35). During the total feeding period (105 d), feeding MON decreased DMI (P ≤ 0.03) compared to VM. Adding sugarcane bagasse to finishing diets during the 20-d adaptation period (ROU) increased ADG (P = 0.05) and G:F (P = 0.03), and tended to increase BW (P = 0.09) compared to NO-ROU. In Exp. 2, 10 ruminally cannulated Nellore steers (BW = 268 ± 38 kg) were used in a completely randomized design to evaluate the effects of the two feed additives used in the Exp. 1 (MON and VM; 5 steers/treatment) on DMI, total apparent digestibility of nutrients, and ruminal fermentation characteristics. No differences in DMI, total tract apparent digestibility of nutrients, and ruminal fermentation characteristics were observed between MON and VM (P ≥ 0.32). An effect of sampling day (P &lt; 0.001) was observed for ruminal pH, which was greater on day 0 compared to day 7, 14, and 21 of the experimental period (P ≤ 0.05). In summary, supplementing monensin and virginiamycin for finishing Nellore bulls fed whole shelled corn diets, resulted in similar growth performance and carcass characteristics. Including sugarcane bagasse to adapt finishing bulls to no-roughage diets containing whole shelled corn is an alternative to increase growth performance.
Knowledge on prevention, diagnosis and treatment of snakebite envenoming among doctors in snakebite-dense regions in Sri Lanka
Authors: Darshani Saumya , Gnanathasan Ariaranee , Arambepola Carukshi , Chang Thashi 
Published: July 2021

Abstract

Background
Sri Lanka is one of the highest envenoming reporting countries globally with &gt;80 000 snakebites per year. Among other factors, knowledge of snakebite among doctors predominantly determines patient outcomes.

Methods
Using a pretested 72-item self-administered questionnaire, we assessed knowledge on identifying common snake species, signs of envenoming and management of venomous snakebites among 280 doctors working in eight state hospitals in regions where snakebite prevalence is highest in Sri Lanka.

Results
Visually, 92.1% correctly identified a cobra and 74.3% identified a Russell's viper, but only 30% could identify a hump-nosed viper (HNV). Syndromic identification of snakes was best for the krait (71.8%) followed by the cobra (59.6%), but poor for the HNV (30%). The median knowledge scores of pictorial and syndromic snake identification, indoor preventive measures and indications of antivenom were &lt;75% of the maximum score. Apart from 62.5% who expected the victim to bring the snake along to the hospital, most doctors selected the correct options of pre-hospital care. The duration of work experience did not influence the competency of syndromic identification. Utilisation of local guidelines was associated with better knowledge in antivenom usage (odds ratio 2.22 [95% confidence interval 1.04 to 5.36]; p=0.03).

Conclusions
Specific deficiencies of core knowledge in snakebite management exist among doctors working in snakebite prevalent regions.
DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches
Authors: Pecina Lukáš , Vďačný Peter 
Published: July 2021

Abstract
Phylogenetically distinct lineages may be hidden behind identical or highly similar morphologies. The phenomenon of morphological crypticity has been recently detected in symbiotic ciliates of the family Clevelandellidae, as multivariate and Fourier shape analyses failed to distinguish genetically distinct taxa. To address the question of species boundaries, the phylogenetic information contained in the rDNA cistron of clevelandellid ciliates, which had been isolated from the digestive tract of blaberid cockroaches, was studied using a multifaceted statistical approach. Multigene phylogenies revealed that the genus Clevelandella is paraphyletic containing members of the genus Paraclevelandia. To resolve the paraphyly of Clevelandella, two new genera, Anteclevelandella gen. nov. and Rhynchoclevelandella gen. nov., are proposed based on morphological synapomorphies and shared molecular characters. Multigene analyses and Bayesian species delimitation supported the existence of 13 distinct species within the family Clevelandellidae, eight of which represent new taxa. Moreover, two new Nyctotherus species were recognized within the clade that is sister to the Clevelandellidae. According to the present distance and network analyses, the first two domains of the 28S rRNA gene showed much higher power for species discrimination than the 18S rRNA gene and ITS region. Therefore, the former molecular marker was proposed to be a suitable group-specific barcode for the family Clevelandellidae.
Personalized Positive End-Expiratory Pressure and Tidal Volume in Acute Respiratory Distress Syndrome: Bedside Physiology-Based Approach
Authors: Mauri Tommaso 
Published: July 2021

OBJECTIVES:
Positive end-expiratory pressure and tidal volume may have a key role for the outcome of patients with acute respiratory distress syndrome. The variety of acute respiratory distress syndrome phenotypes implies personalization of those settings. To guide personalized positive end-expiratory pressure and tidal volume, physicians need to have an in-depth understanding of the physiologic effects and bedside methods to measure the extent of these effects. In the present article, a step-by-step physiologic approach to select personalized positive end-expiratory pressure and tidal volume at the bedside is described.

DATA SOURCES:
The present review is a critical reanalysis of the traditional and latest literature on the topic.

STUDY SELECTION:
Relevant clinical and physiologic studies on positive end-expiratory pressure and tidal volume setting were reviewed.

DATA EXTRACTION:
Reappraisal of the available physiologic and clinical data.

DATA SYNTHESIS:
Positive end-expiratory pressure is aimed at stabilizing alveolar recruitment, thus reducing the risk of volutrauma and atelectrauma. Bedside assessment of the potential for lung recruitment is a preliminary step to recognize patients who benefit from higher positive end-expiratory pressure level. In patients with higher potential for lung recruitment, positive end-expiratory pressure could be selected by physiology-based methods balancing recruitment and overdistension. In patients with lower potential for lung recruitment or in shock, positive end-expiratory pressure could be maintained in the 5–8 cm H2O range. Tidal volume induces alveolar recruitment and improves gas exchange. After setting personalized positive end-expiratory pressure, tidal volume could be based on lung inflation (collapsed lung size) respecting safety thresholds of static and dynamic lung stress. Positive end-expiratory pressure and tidal volume could be kept stable for some hours in order to allow early recognition of changes in the clinical course of acute respiratory distress syndrome but also frequently reassessed to avoid crossing of safety thresholds.

CONCLUSIONS:
The setting of personalized positive end-expiratory pressure and tidal volume based on sound physiologic bedside measures may represent an effective strategy for treating acute respiratory distress syndrome patients.
Cardiopulmonary Exercise Testing in Critically Ill Coronavirus Disease 2019 Survivors: Evidence of a Sustained Exercise Intolerance and Hypermetabolism
Authors: Joris Maurice , Minguet Pauline , Colson Camille , Joris Jean , Fadeur Marjorie , Minguet Gregory , Guiot Julien , Misset Benoit , Rousseau Anne-Françoise 
Published: July 2021

OBJECTIVES:
To investigate exercise capacity at 3 and 6 months after a prolonged ICU stay.

DESIGN:
Observational monocentric study.

SETTING:
A post-ICU follow-up clinic in a tertiary university hospital in Liège, Belgium.

PATIENTS:
Patients surviving an ICU stay greater than or equal to 7 days for a severe coronavirus disease 2019 pneumonia and attending our post-ICU follow-up clinic.

MEASUREMENTS AND MAIN RESULTS:
Cardiopulmonary and metabolic variables provided by a cardiopulmonary exercise testing on a cycle ergometer were collected at rest, at peak exercise, and during recovery. Fourteen patients (10 males, 59 yr [52–62 yr], all obese with body mass index > 27 kg/m2) were included after a hospital stay of 40 days (35–53 d). At rest, respiratory quotient was abnormally high at both 3 and 6 months (0.9 [0.83–0.96] and 0.94 [0.86–0.97], respectively). Oxygen uptake was also abnormally increased at 3 months (8.24 mL/min/kg [5.38–10.54 mL/min/kg]) but significantly decreased at 6 months (p = 0.013). At 3 months, at the maximum workload (67% [55–89%] of predicted workload), oxygen uptake peaked at 81% (64–104%) of predicted maximum oxygen uptake, with oxygen pulse and heart rate reaching respectively 110% (76–140%) and 71% (64–81%) of predicted maximum values. Ventilatory equivalent for carbon dioxide remains within normal ranges. The 50% decrease in oxygen uptake after maximum effort was delayed, at 130 seconds (115–142 s). Recovery was incomplete with a persistent anaerobic metabolism. At 6 months, no significant improvement was observed, excepting an increase in heart rate reaching 79% (72–95%) (p = 0.008).

CONCLUSIONS:
Prolonged reduced exercise capacity was observed up to 6 months in critically ill coronavirus disease 2019 survivors. This disability did not result from residual pulmonary or cardiac dysfunction but rather from a metabolic disorder characterized by a sustained hypermetabolism and an impaired oxygen utilization.
Enorma shizhengliae sp. nov. and Eggerthella guodeyinii sp. nov., two new members of the family Coriobacteriaceae
Authors: Ge Yajun , Yang Jing , Lai Xin-He , Jin Dong , Lu Shan , Zhang Gui , Huang Ying , Luo Xuelian , Zheng Han , Tao Yuanmeihui , Yuan Tingting , Li Lianfeng , Zhang Xiaoyan , Xu Jianguo 
Published: July 2021

Four obligatory anaerobic, Gram-stain-positive, non-motile and rod-shaped organisms (HF-1365T, HF-1362, HF-1101T and HF-4214) were isolated from faecal samples of healthy Chinese subjects. Results of 16S rRNA gene sequence analyses showed that these isolates belong to the genera

Enorma

(strains HF-1365T and HF-1362) and

Eggerthella

(strains HF-1101T and HF-4214), closest to

Enorma massiliensis

(both 98.6 %) and

Eggerthella sinensis

(98.0 and 97.8 %), respectively. The whole genome sequences of strains HF-1365T and HF-1101T were 2.3 and 4.2 Mb in size with 61.7 and 66.2 mol% DNA G+C content, respectively. The average nucleotide identity and digital DNA–DNA hybridization values indicated that strains HF-1365T and HF-1101T represent novel species in the genera

Enorma

and

Eggerthella

. Major fatty acid constituents (>10 %) of strains HF-1365T and HF-1362 were C12 : 0 (24.7 and 23.9 %), C14 : 0 (21.9 and 20.6 %) and summed feature 1 (C15 : 1iso H/C13 : 0 3OH; 12.8 and 10.8 %); those of strains HF-1101T and HF-4214 were C18 : 1
ω9c (32.4 and 33.1 %) and C16 : 0 (13.9 and 14.0 %). Strain HF-1365T had phospholipid, glycolipid, lipid and phosphoglycolipid without any known quinones, while strain HF-1101T had diphosphatidylglycerol as the major polar lipid and MK-7 (80.7 %) as the predominant quinone. On the basis of their phylogenetic and phenotypic characteristics, strains HF-1365T and HF-1101T represent two distinct species, respectively, in the genera

Enorma

and

Eggerthella

, for which the names Enorma shizhengliae sp. nov. (type strain HF-1365T=CGMCC 1.17435T=GDMCC 1.1705T=JCM 33601T) and Eggerthella guodeyinii sp. nov. (type strain HF-1101T=CGMCC 1.17436T=GDMCC 1.1668T=JCM 33773T) are proposed.
SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data
Authors: Zhang Yunwei , Wong Germaine , Mann Graham , Muller Samuel , Yang Jean Y.H. 
Published: July 2021

AbstractSurvival analysis is a branch of statistics that deals with both, the tracking of time and of the survival status simultaneously as the dependent response. Current comparisons of survival model performance mostly center on clinical data with classic statistical survival models, with prediction accuracy often serving as the sole metric of model performance. Moreover, survival analysis approaches for censored omics data have not been thoroughly investigated. The common approach is to binarise the survival time and perform a classification analysis.Here, we develop a benchmarking framework, SurvBenchmark, that evaluates a diverse collection of survival models for both clinical and omics datasets. SurvBenchmark not only focuses on classical approaches such as the Cox model, but it also evaluates state-of-art machine learning survival models. All approaches were assessed using multiple performance metrics, these include model predictability, stability, flexibility and computational issues. Our systematic comparison framework with over 320 comparisons (20 methods over 16 datasets) shows that the performances of survival models vary in practice over real-world datasets and over the choice of the evaluation metric. In particular, we highlight that using multiple performance metrics is critical in providing a balanced assessment of various models. The results in our study will provide practical guidelines for translational scientists and clinicians, as well as define possible areas of investigation in both survival technique and benchmarking strategies.Contactjean.yang@sydney.edu.au
Collaborations and deceptions in strategic interactions revealed by hyperscanning fMRI
Authors: Shen Siao-Shan , Cheng Jen-Tang , Hsu Yi-Ren , Chen Der-Yow , Weng Ming-Hung , Kung Chun-Chia 
Published: July 2021

AbstractDespite its ubiquity, deceiving as a social phenomenon is scarcely addressed with fMRI, partly due to the spontaneity and individual differences in cheating, and the contextual variability that fosters lying. In this hyperscanning fMRI study, the participant pairs (n=33) from Taipei and Tainan joined an opening-treasure-chest (OTC) game, where the dyads took alternative turns as senders (to inform) and receivers (to decide) for guessing the right chest. The cooperation condition was achieved by, upon successful guessing, splitting the $200NTD trial reward, thereby promoting mutual trust. The competition condition, in contrast, was done by, also upon winning, the latter receivers taking all the $150NTD reward, thereby encouraging strategic interactions. One key fMRI finding was the negative correlations between the connectivity of the right temporo-parietal junction (rTPJ), known as the theory-of-mind function, and amygdala, parahippocampal gyrus, and rostral anterior cingulate (rACC), to senders’ behavioral lying rates. Furthermore, the Multi-Voxel Pattern Analysis (MVPA) over multiple searchlight-identified Region-Of-Interests (ROIs), in classifying either the “truthful vs. lying in $150” or the “truthful in $200 vs. truthful in $150” conditions achieved 61% and 84.5% accuracy, respectively, reflecting the idiosyncratic brain networks involved in distinguishing the social trust vs. deceptions in the dyadic interactions.
Parallel Framework for Inferring Genome Scale Gene Regulatory Networks
Authors: Sebastian Softya , Roy Swarup 
Published: July 2021

AbstractGenome-scale network inference is essential to understand comprehensive interaction patterns. Current methods are limited to the reconstruction of small to moderate-size networks. The most obvious alternative is to propose a novel method or alter existing methods that may leverage parallel computing paradigms. Very few attempts also have been made to re-engineer existing methods by executing selective iterative steps concurrently. We propose a generic framework in this paper that leverages parallel computing without re-engineering the original methods. The proposed framework uses state-of-the-art methods as a black box to infer sub-networks of the segmented data matrix. A simple merger was designed based on preferential attachment to generate the global network by merging the sub-networks.Fifteen (15) inference methods were considered for experimentation. Qualitative and speedup analysis was carried out using DREAM challenge networks. The proposed framework was implemented on all the 15 inference methods using large expression matrices. The results were auspicious as we could infer large networks in reasonable time without compromising the qualitative aspects of the original (serial) algorithm.CLR, the top performer, was then used to infer the network from the expression profiles of an Alzheimer’s disease (AD) affected mouse model consisting of 45,101 genes. We have also highlighted few hub genes from the network that are functionally related to various diseases.