bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting Genomic Determinants of Positive Selection with an Evolution-Guided Regression Model
Authors: Huang Yi-Fei 
Published: September 2021

Abstract
In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald–Kreitman (MK) test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the MK test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their nonmetabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation.
CancerSCEM: a database of single-cell expression map across various human cancers
Authors: Zeng Jingyao , Zhang Yadong , Shang Yunfei , Mai Jialin , Shi Shuo , Lu Mingming , Bu Congfan , Zhang Zhewen , Zhang Zaichao , Li Yang , Du Zhenglin , Xiao Jingfa 
Published: September 2021

Abstract
With the proliferating studies of human cancers by single-cell RNA sequencing technique (scRNA-seq), cellular heterogeneity, immune landscape and pathogenesis within diverse cancers have been uncovered successively. The exponential explosion of massive cancer scRNA-seq datasets in the past decade are calling for a burning demand to be integrated and processed for essential investigations in tumor microenvironment of various cancer types. To fill this gap, we developed a database of Cancer Single-cell Expression Map (CancerSCEM, https://ngdc.cncb.ac.cn/cancerscem), particularly focusing on a variety of human cancers. To date, CancerSCE version 1.0 consists of 208 cancer samples across 28 studies and 20 human cancer types. A series of uniformly and multiscale analyses for each sample were performed, including accurate cell type annotation, functional gene expressions, cell interaction network, survival analysis and etc. Plus, we visualized CancerSCEM as a user-friendly web interface for users to browse, search, online analyze and download all the metadata as well as analytical results. More importantly and unprecedentedly, the newly-constructed comprehensive online analyzing platform in CancerSCEM integrates seven analyze functions, where investigators can interactively perform cancer scRNA-seq analyses. In all, CancerSCEM paves an informative and practical way to facilitate human cancer studies, and also provides insights into clinical therapy assessments.
Assembly Apparatus of Light-Harvesting Complexes: Identification of Alb3.1–cpSRP–LHCP Complexes in the Green Alga Chlamydomonas reinhardtii
Authors: Rathod Mithun Kumar , Nellaepalli Sreedhar , Ozawa Shin-Ichiro , Kuroda Hiroshi , Kodama Natsumi , Bujaldon Sandrine , Wollman Francis-André , Takahashi Yuichiro 
Published: September 2021

Abstract
The unicellular green alga, Chlamydomonas reinhardtii, contains many light-harvesting complexes (LHCs) associating chlorophylls a/b and carotenoids; the major LHCIIs (types I, II, III and IV) and minor light-harvesting complexes, CP26 and CP29, for photosystem II, as well as nine LHCIs (LHCA1–9), for photosystem I. A pale green mutant BF4 exhibited impaired accumulation of LHCs due to deficiency in the Alb3.1 gene, which encodes the insertase involved in insertion, folding and assembly of LHC proteins in the thylakoid membranes. To elucidate the molecular mechanism by which ALB3.1 assists LHC assembly, we complemented BF4 to express ALB3.1 fused with no, single or triple Human influenza hemagglutinin (HA) tag at its C-terminus (cAlb3.1, cAlb3.1-HA or cAlb3.1–3HA). The resulting complemented strains accumulated most LHC proteins comparable to wild-type (WT) levels. The affinity purification of Alb3.1-HA and Alb3.1–3HA preparations showed that ALB3.1 interacts with cpSRP43 and cpSRP54 proteins of the chloroplast signal recognition particle (cpSRP) and several LHC proteins; two major LHCII proteins (types I and III), two minor LHCII proteins (CP26 and CP29) and eight LHCI proteins (LHCA1, 2, 3, 4, 5, 6, 8 and 9). Pulse-chase labeling experiments revealed that the newly synthesized major LHCII proteins were transiently bound to the Alb3.1 complex. We propose that Alb3.1 interacts with cpSRP43 and cpSRP54 to form an assembly apparatus for most LHCs in the thylakoid membranes. Interestingly, photosystem I (PSI) proteins were also detected in the Alb3.1 preparations, suggesting that the integration of LHCIs to a PSI core complex to form a PSI–LHCI subcomplex occurs before assembled LHCIs dissociate from the Alb3.1–cpSRP complex.
Salinity changes may influence dinoflagellate cyst morphometry: data from monsoon-influenced tropical coastal ecosystems
Authors: Rodrigues Roy Valentino , Patil Jagadish Siddalingappa 
Published: September 2021

Abstract
Generally, dinoflagellate cyst morphology is species specific. Their variability due to environmental factors (temperature and salinity) makes them potential proxies for such factors. However, there is a dearth of information on the variability of cyst morphology from monsoon-influenced coastal ecosystems. This study on distribution and variability in the dinocyst morphometry of Pyrophacus steinii and Protoperidinium pentagonum from estuarine (Cochin port and Zuari estuary) and marine (New Mangalore port) ecosystems along the Indian west coast revealed that both are common and euryhaline species. However, variability in cyst morphometry was observed and correlated salinity values between the ecosystems. Other parameters (i.e. the prevalence of narrow temperature ranges and nutrient-rich conditions) may not be dominant in influencing cysts morphometry. Cyst length, breadth and processes length (only in P. steinii) of both were relatively larger and smaller at salinity ranges higher and lower than 25 psu, respectively. The data presented for different ecosystems are comparable in most parameters except salinity variations. This study extends the ranges of records for both species. Pyrophacus steinii cysts were significantly larger (up to 120 μm in Zuari estuary) than literature reports on cysts from higher salinity systems and salinity-related variability in P. pentagonum cyst size indicates notable potential proxy indicator of salinity.
Drivers of microplankton community assemblage following tropical cyclones
Authors: Fiorendino James M , Gaonkar Chetan C , Henrichs Darren W , Campbell Lisa 
Published: September 2021

AbstractTropical cyclones impose tremendous impacts on microplankton communities. When Hurricane Harvey struck Texas in August 2017, delivering record rainfall, the resulting historically large freshwater plume provided an opportunity to identify how the coastal microplankton community responded to such a drastic shift in hydrography. Two cruises were conducted along the Texas coast one week apart to assess the impact of the low-salinity plume moving downcoast. The spatial–temporal variability and recovery of the microplankton community was compared with microplankton community changes during and after 13 other tropical storm/cyclone events observed during the decade-long record from the Texas Observatory for Algal Succession Timeseries (TOAST). Results revealed an unprecedented ciliate-dominated community developed in the weeks following Hurricane Harvey. TOAST data revealed diatoms dominated during upwelling and water column mixing. Moderate downwelling conditions favored dinoflagellates while strong downwelling and reduced salinity following Hurricane Harvey resulted in a ciliate-dominated community. The unexpectedly large biomass of ciliates and low diatom biomass observed during the response cruise indicated that the microplankton community had not yet recovered. Intensification of future hurricanes may produce brief blooms of diatoms, while dinoflagellates or ciliates dominate following high freshwater discharge. These drastic shifts in microplankton communities pose important implications for biogeochemical cycling, trophic interactions and commercial fisheries.
A New Generation of Police Officers: Experiences of Student Officers Undertaking the Police Constable Degree Apprenticeship in One UK Police Force
Authors: Watkinson-Miley Charlotte , Cox Carol , Deshpande Maya 
Published: September 2021

Abstract
The Policing Vision 2025 and 2030 outlined long-term strategies to ensure consistency and accreditation in those joining policing careers in England and Wales, standardizing the qualifications obtained by all new recruits. The Police Educational Qualifications Framework has since been designed to support this vision, enabling three new entry routes into policing, one being the Police Constable Degree Apprenticeship. This resulted in policing becoming a graduate profession from 2020, which is argued to be a radical transformation for policing. This research conducted focus groups and thematic analysis with three cohorts of student police officers (N = 30) undertaking the Police Constable Degree Apprenticeship (PCDA) at different stages of their programme in one police force. It unpicked motivations for joining the PCDA, their experiences so far and improvements for future workings of the programme. The disconnect between policing and academia was a key barrier, and students could not always utilize the academic teaching in practical policing settings.
Occupational risk of COVID-19 by country of birth. A register-based study
Authors: Kjøllesdal Marte , Magnusson Karin 
Published: September 2021

AbstractBackgroundOccupational exposure has been suggested to contribute to a disproportionate burden of COVID-19 among immigrants. We aim to assess this hypothesis in Norway.MethodsIn 2729 627 adults born in Norway, Somalia, Pakistan, Iraq, Afghanistan and Turkey, we examined whether persons employed as taxi drivers, bus and tram drivers, child care workers, nurses, personal care workers in health, food service counter attendants, waiters/bartenders, cleaners and shop sale persons had a higher risk of COVID-19, from 1 April 2020 to 2 December 2020, compared with (i) Norwegian-born in the same occupational group and (ii) all others with the same birth country and aged 20–70 years, using logistic regressions.ResultsWithin each occupational group, immigrants had a greatly increased odds of COVID-19 when compared with Norwegian-born (odds ratio [OR] ~ 1.66–12.72). However, immigrants working in the selected occupations had the same odds of COVID-19 as person with same birth country not having the same occupation (OR ~ 1). Exceptions were Somalian, Afghani and Iraqi personal care workers in health services who had an increased odds of COVID-19 compared with others from the same country.ConclusionOccupation is not an important driver of the high rates of COVID-19 among immigrants from Somalia, Pakistan, Iraq, Afghanistan and Turkey.
Social media use is linked to poor sleep quality: The opportunities and challenges to support evidence-informed policymaking in the UAE
Authors: Al Kazhali Manar , Shahwan Moyad , Hassan Nageeb , Jairoun Ammar Abdulrahman 
Published: September 2021

AbstractBackgroundThis study was conducted among a convenience sample of Ajman University students in UAE between February 2018 and May 2019.MethodsAll undergraduate and master’s degree students from the 1st to 5th year of medical and non-medical colleges. The survey was carried out by distributing a pre-designed, pre-structured questionnaire to the students during lectures. The questionnaires were primarily composed of three sections: demographic characteristics, educational characteristics and sleep quality characteristics. The data were analyzed using STATA version 14.2. Logistic regression analysis was used to investigate the association between sleep characteristics, social media use and other significant risk factors. The P-values &lt; 0.05 were considered to be statistically significant.ResultsThe vast majority of the study participants were social media users, and a considerable proportion suffered from poor sleep quality. A significantly increased risk of bad sleep quality and intermittent/anxious sleep patterns were observed among social media users.ConclusionHealth policymakers should fully consider these factors in improving the sleep quality of university students.
Venom of the desert black snakeWalterinnesia aegyptiaenhances anti-tumor immunity via its beneficial modulatory effects on pro- and anti-tumorigenic inflammatory mediators in cultured colon cancer cells
Authors: Daghestani Maha H , Ambreen Khushboo , Hakami Hana H , Omair Mohammed A , Saleem Abdulaziz M , Aleisa Nadia A , AlNeghery Lina M , Amin Mohannad H , Alobaid Hussah M , Omair Maha A , Hassen Lena M 
Published: September 2021

AbstractThe role of inflammation in colon cancer is understood as a well-accepted factor that has the tendency to release multiple pro- and anti-tumorigenic inflammatory mediators. Inflammation-induced increased expression of anti-tumorigenic inflammatory mediators and decreased expression of pro-tumorigenic inflammatory mediators encourage beneficial inflammatory effects in terms of powerful anti-tumor immunity. The present study aims to screen the beneficial inflammatory effects of Walterinnesia aegyptia venom via determining its modulatory tendency on the expression of 40 pro- and anti-tumorigenic inflammatory mediators (cytokines/growth factors/chemokines) in LoVo human colon cancer cell line. LoVo-cells were treated with varying doses of crude venom of W. aegyptia. Cell viability was checked utilizing flow cytometry, and IC50 of venom was determined. Venom-induced inflammatory effects were evaluated on the expression of 40 different inflammatory mediators (12 anti-tumorigenic cytokines, 11 pro-tumorigenic cytokines, 7 pro-tumorigenic growth factors, 9 pro-tumorigenic chemokines and 1 anti-tumorigenic chemokine) in treated LoVo-cells [utilizing enzyme-linked immunosorbent assay (ELISA)] and compared with controls. Treatment of venom induced significant cytotoxic effects on inflamed LoVo-cells. IC50 treatment of venom caused significant modulations on the expression of 22 inflammatory mediators in treated LoVo-cells. The beneficial modulatory effects of venom were screened via its capability to significantly increase the expression of five powerful anti-tumorigenic mediators (IL-9, IL-12p40, IL-15, IL-1RA and Fractalkine) and decrease the expression of four major pro-tumorigenic mediators (IL-1β, VEGF, MCP-1 and MCP-3). Walterinnesia aegyptia venom-induced beneficial modulations on the expression of nine crucial pro/anti-tumorigenic inflammatory mediators can be effectively used to enhance powerful anti-tumor immunity against colon cancer.
Mitochondrial sequences of the extinct Cypriot pygmy hippopotamus confirm its phylogenetic placement
Authors: Psonis Nikolaos , Vassou Despoina , Nicolaou Loucas , Roussiakis Socrates , Iliopoulos George , Poulakakis Nikos , Sfenthourakis Spyros 
Published: September 2021

Abstract
The Cypriot pygmy hippopotamus is an extinct Mediterranean species that inhabited the island of Cyprus during the Late Pleistocene. This iconic species last appears at the archaeological site of Akrotiri Aetokremnos, dated to ~12 500 cal. BP. Taxonomically, the Cypriot pygmy hippopotamus has been assigned to Hippopotamus minor, which, based on morphology, is more closely related to the common hippopotamus (Hippopotamus amphibius; today present only in Sub-Saharan Africa) than to the West African pygmy hippopotamus (Choeropsis liberiensis). Despite adverse conditions for preservation that greatly reduce the likelihood of DNA preservation in subfossil samples from hot environments, we recovered and analysed ancient DNA from petrous bones excavated from Akrotiri Aetokremnos. By whole mitogenome hybridization capture and exhaustive high-throughput sequencing, we were able to investigate the molecular phylogeny and taxonomic status of the Cypriot pygmy hippopotamus. The results of our low-coverage ancient mitogenomic analyses support the close phylogenetic affinity of H. minor to H. amphibius, with their divergence estimated at ~1.36 or 1.58 Mya, depending on the molecular dating method. To our knowledge, this study constitutes the first step towards reconstruction of the molecular phylogeny of Mediterranean Hippopotaminae.
Phylogeny of the new subfamily Cladodinae: neotenic fireflies from the Neotropics (Coleoptera: Lampyridae)
Authors: Bocakova Milada , Campello-Gonçalves Lucas , Da Silveira Luiz Felipe Lima 
Published: September 2021

AbstractPhylogenetic relationships of Vestini with extensive sampling were inferred using 37 taxa scored for 66 morphological characters. Consistent with recent DNA analyses, Vesta is found to be sister to Photurinae rendering Vestini monotypic. Conversely, our parsimony and model-based analyses robustly support the new subfamily Cladodinae established for Neotropical species of the former Vestini. The cladodine lineage includes Cladodes, Dodacles, Dryptelytra, Ledocas, plus the newly proposed Andecladodes gen. nov. and Brasilocladodes gen. nov. While Ledocas is mostly paraphyletic, Cladodes is polyphyletic and, therefore, Cladodes s.s. is introduced. Further, most trees presented a distinct Nyctocrepis, which is revalidated and includes the subgenus Fenestratocladodes (transferred from Cladodes). Finally, a highly supported crown clade designated as the Dodacles lineage is regularly recovered, splitting into two sister-clades: (1) Dodacles, Brasilocladodes and (2) Dryptelytra, C. proteus, C. solieri and Andecladodes. Four new Andean species are described: Andecladodes cosangensis sp. nov., A. ovalis sp. nov., Dryptelytra pampahermosae sp. nov. and Ledocas pikillactanus sp. nov. To recover the monophyly of genera, the following new combinations are proposed: Brasilocladodes carinatuscomb. nov., Brasilocladodes delalandeicomb. nov., Brasilocladodes illigericomb. nov., Dodacles lateraliscomb. nov. and Dodacles nigercomb. nov. (transferred from Cladodes); Ledocas emissuscomb. nov., Ledocas remixtuscomb. nov. (from Dodacles); Cladodes proteus comb. nov. (from Ledocas) Nyctocrepis malleri comb. nov. and Nyctocrepi stellatacomb. nov. (from Cladodes); and Cladodes cincticolliscomb. nov. and Cladodes melanuruscomb. nov. (from Vesta).
Redescription of the hermit crabDiogenes pugilator(Decapoda: Anomura) reveals the existence of a species complex in the Atlanto-Mediterranean transition zone, resulting in the resurrection ofD. curvimanusand the description of a new species
Authors: Almón Bruno , Cuesta Jose A , Schubart Christoph D , Armenia Lisa , Enrique García-Raso J 
Published: September 2021

AbstractExamination of material from the coasts of the Iberian Peninsula and nearby areas has revealed that more than one species is mixed under the name for the common diogenid hermit crab, Diogenes pugilator. In this study, three species are recognized, primarily on the basis of a combination of morphological characters and live colour patterns. Diogenes pugilator is redescribed on the basis of a neotype selected from near the supposed type locality, as well as specimens from other localities. Diogenes curvimanus is resurrected and the name attributed to a second species, whereas a third morphotype is described as a new species, Diogenes armatus sp. nov.. The last two species are also fully described and differentiating characters among the three species are discussed. Newly generated sequences from two mitochondrial genes and one nuclear gene, and comparative analyses with other available DNA sequences for the genus, are also included. The corresponding molecular phylogenies support the recognition of the three species and suggest the presence of additional unknown species in the D. pugilator species complex. All previous records of D. pugilator should be revised in the light of these new findings. Finally, a comprehensive identification key to the eastern Atlantic and western Mediterranean species of Diogenes is also provided.
Clinical Trial of Efficacy and Toxicity of Disoproxil Tenofovir Fumarate and Emtricitabine for Mild to Moderate SARS-CoV-2 Infections
Authors: Arruda E.A.G. , Pires-Neto R.J. , Medeiros M.S. , Quirino-Filho J. , Clementino M. , Gondim R.N.D.G. , Magalhães L.M.V.C. , Cavalcante K.F. , Viana V.A.F. , Mello Liana Perdigão , Martins R.B , Santos A.A. , Magalhães P.J.C. , Havt A. , Lopes N.P. , Arruda-Neto E. , Lima A.A.M. ,   study group members
Published: September 2021

AbstractThis study aimed to evaluate the efficacy and toxicity of tenofovir (TDF) and TDF combined with emtricitabine (TDF/FTC) in patients with mild to moderate COVID-19 infections. We conducted a randomized, double-blind, placebo-controlled clinical trial in patients with clinical suspicion of mild to moderate respiratory infection caused by SARS-CoV-2 who were treated at an outpatient clinic. Patients were randomly recruited to take 10 days of TDF (300 mg/day), TDF (300 mg/day) combined with FTC (200 mg/day) or placebo Vitamin C (500 mg/day). The primary parameter was the score of symptoms and predictive signs of COVID-19, assessed on the seventh day of patient follow-up. From a total of 309 patients with clinical suspicion of SARS-CoV-2, 227 met the inclusion criteria and were randomly distributed into the following groups: (a) 75 (one did not initiate treatment) in the TDF group; (b) 74 in the TDF combined with FTC group; and (c) 77 in the Vitamin C group (placebo). Of the 226 patients, 139 (62%) were positive for SARS-CoV-2. Fever (≥37.8°C), ageusia or dysgeusia, anosmia or dysosmia, and two or more clinical symptoms or signs were significantly associated with SARS-CoV-2 infection. There was no significant change in clinical score based on clinical symptoms and signs between treatment groups. Patients with mild to moderate infection by SARS-CoV-2 had higher concentrations of G-CSF, IL-1β, IL-6 and TNF-α compared to patients without infection. Patients with mild to moderate respiratory infection, with fever (≥37.8°C), loss of smell, loss of taste and two or more symptoms, have a better prediction for the diagnosis of COVID-19. Patients with SARS-CoV-2 showed higher and more persistent proinflammatory cytokines profile compared to patients not infected with SARS-CoV-2. Pharmacological intervention with TDF or TDF combined with FTC did not change the clinical signs and symptoms score in mild to moderate respiratory infection in patients with SARS-CoV-2 compared to the Vitamin C group (placebo).