bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 Vpr counteracts HLTF-mediated restriction of HIV-1 infection in T cells
Authors: Yan Junpeng , Shun Ming-Chieh , Zhang Yi , Hao Caili , Skowronski Jacek 
Published: April 2019

Significance
An obligatory step in the replication cycle of all retroviruses involves reverse transcription of their RNA genomes into double-stranded DNA for integration into the host cell chromosome. The process of synthesizing double-stranded HIV-1 DNA is carried out by viral reverse transcriptase, which lacks some of the enzymatic activities necessary to accomplish this task. Thus, the process is completed by cellular postreplication DNA repair enzymes. Here, we report that select aspects of the cellular postreplication DNA machinery restrict HIV-1 replication in dividing T cells and that these restrictions are counteracted by HIV-1 Vpr accessory virulence factor. Our studies reveal that specific cellular postreplication DNA repair enzymes can sense and inhibit HIV-1 infection, and hence constitute a class of HIV-1 restriction factors.
Exploring the use of translanguaging to measure the mathematics knowledge of emergent bilingual students
Authors: Lopez Alexis A. , Guzman-Orth Danielle , Turkan Sultan 
Published: April 2019

AbstractThe study reported in this article investigated the design and implementation of a flexible bilingual mathematics assessment that allows for translanguaging whenever needed, to help the mathematics knowledge of emergent bilingual students emerge. The assessment included 10 mathematics items, six selected-response and four constructed-response items, which were enhanced with dual language supports such as seeing and listening to the items, writing or saying a response, and showing synonyms for certain words, all in English, Spanish, or any combination of both languages. These supports allow test takers to draw on their entire linguistic repertoire and their full range of linguistic practices to demonstrate their knowledge and skills in mathematics. Ten emergent bilingual students participated in cognitive interviews designed to collect data on usability and perception of the usefulness of the dual language supports. It was found that students were able to use the available supports strategically whenever needed, used their entire linguistic repertoire to complete the items, and had a positive perception of the supports.
Towards a better understanding of the link between executive functions, early literacy, and emergent mathematical
abilities
Authors: Schwarz Mila , Shaul Shelley 
Published: April 2019

Abstract
The aim of the current study was two-fold. It aimed (i) to examine how a multi-component task, as well as more
specific executive function (EF) tasks, are related to a wide range of early literacy (phonological awareness, orthographic
knowledge, word writing) and emergent mathematical abilities; and (ii) to broaden our understanding of the similar
(domain-general) or differential (domain-specific) nature of these relations. The study was conducted in the northern part of
Israel. Our results indicated that the multi-component task Head-Toes-Knees-Shoulders, which taps most EF
components (attentional control, inhibition, shifting, and working memory) significantly contributed to most domains of preschool
academic development. These included orthographic knowledge and emergent mathematical abilities even after controlling for the
role of background cognitive skills.
The findings showed that EF tasks have domain-general predictive power for pre-academic abilities that are less
automatic and require more effortful processing of information such as word writing at preschool age. Moreover, our results
provide clear empirical evidence for the psychometric validity of the multi-component task as a tool that can assess individual
differences in EFs for the early identification of children at risk for academic difficulties. This finding can contribute to
practitioners searching for an ecologically valid, age-appropriate, and age-sensitive measure of EF abilities as a diagnostic
tool.
Ruminal fluids as substrate for investigating production diseases of small and large ruminant species.
Authors: Filipe J. F. S. , Riva F. , Bani P. , Trevisi E. , Amadori M. 
Published: April 2019

Abstract
Production diseases are a huge problem for high-yielding dairy cows, especially during the post-calving period when a negative energy balance is present and the animals are unable to achieve enough feed energy intake to match their high requests. Correct management of production diseases demands an early diagnostic approach and prognostic parameters. In ruminants, metabolic stress greatly influences forestomach physiology, including immune responses. Therefore a proper evaluation of production diseases in ruminants should also include markers of the innate immune response to metabolic stress. New studies suggest that forestomach immune responses could be focused to 'dangers' arising in the rumen (diet unbalance, abnormal fermentations), but also arise as reporter system of disease conditions elsewhere in the body. This means that ruminal fluids could be useful diagnostic specimens, and their immune markers could integrate consolidated diagnostic parameters (e.g. rumen pH and volatile fatty acids, milk cell counts, blood, faecal analytes) and contribute to robust, early diagnosis of production diseases in dairy cattle.
Amplitude of the circadian rhythm of temperature in homeotherms.
Authors: Maloney S. K. , Goh G. , Fuller A. , Vesterdorf K. , Blache D. 
Published: April 2019

Abstract
In most endothermic homeotherms, core body temperature follows a circadian rhythm. This review focuses on the amplitude of the circadian rhythm of body temperature (CRT) because the amplitude of the CRT has received increasing attention in the last few years. First, we discuss the methodology that can be used to measure the CRT, and the methodology used to calculate the amplitude of the CRT. Then, we illustrate the effect of changes in the external and internal environments on the amplitude of the CRT. Quite interestingly, as illustrated in this paper, while the molecular and hormonal basis of the CRT is well understood, the control of the amplitude is not. We conclude that challenges in the capacity of the animal to thermoregulate, or to manage energy, can impact on the amplitude of the CRT.
An experimental apparatus to measure soot morphology at high pressures using multi-angle light scattering
Authors: Amin Hafiz M F , Roberts William L 
Published: April 2019

Abstract
In this work, a novel experimental setup is described which is designed and built specifically to study soot morphology using light scattering and extinction techniques at elevated pressures. The experimental setup consists of a counterflow burner housed inside a pressure vessel. A unique feature of this pressure vessel is the four curved optical windows which can provide the required optical access for light scattering measurements in order to infer the morphological parameters of soot. Using this setup, N
2-diluted ethylene and air counterflow flames are stabilized from 3 to 5 atm. Global strain rate (a) of 30 s−1 is maintained at all conditions and all the flames studied are soot formation (SF) flames. Light scattering by soot is measured between 15° to 165° at different locations along the axis of the burner. Ratio of total scattering to absorption (ρ
sa), path averaged soot volume fraction (f
v), mean primary particle size (d
p), mean radius of gyration of aggregates (R
gm) and fractal dimension (D
f) are calculated from multi-angle light scattering and extinction data using Rayleigh–Debye–Gans theory for fractal aggregates (RDG-FA). ρ
sa, f
v, d
p, and R
gm increase as the pressure is raised. The scattering contribution in these measurements vary from 1.3% to 16% of absorption which suggests that wide angle optical access is essential for accurate measurements of f
v. D
f equal to 1.27 is measured near the flame at 3 atm which increases as the particles are convected away from the flame and D
f increases to 1.98 at 5 atm.
ENSO drives near-surface oxygen and vertical habitat variability in the tropical Pacific
Authors: Leung Shirley , Thompson LuAnne , McPhaden Michael J , Mislan K A S 
Published: April 2019

AbstractEl Niño-Southern oscillation (ENSO) is the leading cause of sea surface temperature variability in the tropical Pacific with known impacts on tuna geographic range, but its effects on oxygen and available oxygenated habitat space are less clear. Variations in oxygenated vertical habitat space in the upper-ocean can alter interactions between predator and prey, as well as drive changes in the vulnerability of economically important tuna and other pelagic fish to surface fishing gear. Usingin situmeasurements, we show that ENSO is the primary driver of upper-ocean oxygen partial pressure (pO2) variability on year-to-year time scales in the tropical Pacific. Mechanistically, these pO2variations are primarily caused by vertical shifts in thermocline depth, which alternately elevate and depress cold, hypoxic waters from the ocean interior depending on the ENSO phase and location. Transport-driven, isopycnal pO2variations within the thermocline also play an important but secondary role. In the western tropical Pacific, waters within the exclusive economic zones of Palau, Micronesia, Nauru, and the Marshall Islands undergo the greatest variations in oxygenated tuna vertical habitat extent: approximately 19.5 m, 23.9 m, 19.5 m, and 19.3 m, respectively, between El Niño and La Niña phases. Oxygen thus plays an important role in altering available tuna vertical habitat space between different phases of ENSO.
An update on the thermosteric sea level rise commitment to global warming
Authors: Hieronymus Magnus 
Published: April 2019

Abstract
The equilibrium thermosteric sea level rise caused by global warming is evaluated in several coupled climate models. The thermosteric sea level rise is found to be well approximated as a linear function of the mean ocean temperature increase in the models. However, the mean ocean temperature increase as a function of the mean surface temperature increase differs between the models. Our models can be divided into two branches; models with an Atlantic meridional overturning circulation that increases with warming have large mean ocean temperature increases and vice versa. These two different branches give estimates of the equilibrium thermosteric sea level rise per degree of surface warming that are respectively 98% and 21% larger than the estimate given in the IPCC Fifth Assessment Report. Our estimates of the equilibrium thermosteric sea level rise are also used to infer an equilibrium sea level sensitivity, a parameter akin to the often used equilibrium climate sensitivity metric.
Rank reduction of string C-group representations
Authors: Brooksbank Peter , Leemans Dimitri 
Published: April 2019

We show that a rank reduction technique for string C-group representations first used in [Adv. Math. 228 (2018), pp. 3207–3222] for the symmetric groups generalizes to arbitrary settings. The technique permits us, among other things, to prove that orthogonal groups defined on

d
d

-dimensional modules over fields of even order greater than 2 possess string C-group representations of all ranks

3
⩽
n
⩽
d

3\leqslant n\leqslant d

. The broad applicability of the rank reduction technique provides fresh impetus to construct, for suitable families of groups, string C-groups of highest possible rank. It also suggests that the alternating group

Alt
⁡
(
11
)

\operatorname {Alt}(11)

—the only known group having “rank gaps”—is perhaps more unusual than previously thought.
A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies
Authors: Tang Jing , Wang Yunxia , Fu Jianbo , Zhou Ying , Luo Yongchao , Zhang Ying , Li Bo , Yang Qingxia , Xue Weiwei , Lou Yan , Qiu Yunqing , Zhu Feng 
Published: April 2019

Abstract
Microbial community (MC) has great impact on mediating complex disease indications, biogeochemical cycling and agricultural productivities, which makes metaproteomics powerful technique for quantifying diverse and dynamic composition of proteins or peptides. The key role of biostatistical strategies in MC study is reported to be underestimated, especially the appropriate application of feature selection method (FSM) is largely ignored. Although extensive efforts have been devoted to assessing the performance of FSMs, previous studies focused only on their classification accuracy without considering their ability to correctly and comprehensively identify the spiked proteins. In this study, the performances of 14 FSMs were comprehensively assessed based on two key criteria (both sample classification and spiked protein discovery) using a variety of metaproteomics benchmarks. First, the classification accuracies of those 14 FSMs were evaluated. Then, their abilities in identifying the proteins of different spiked concentrations were assessed. Finally, seven FSMs (FC, LMEB, OPLS-DA, PLS-DA, SAM, SVM-RFE and T-Test) were identified as performing consistently superior or good under both criteria with the PLS-DA performing consistently superior. In summary, this study served as comprehensive analysis on the performances of current FSMs and could provide a valuable guideline for researchers in metaproteomics.
Uptake of D-xylose and L-arabinose in Haloferax volcanii involves an ABC transporter of the CUT1 subfamily
Authors: Johnsen Ulrike , Ortjohann Marius , Sutter Jan-Moritz , Geweke Sarah , Schönheit Peter 
Published: April 2019

ABSTRACT
Haloferax volcanii degrades D-xylose and L-arabinose via an oxidative pathway to α-ketoglutarate as an intermediate. The enzymes of this pathway are encoded by the xac gene cluster (xylose and arabinose catabolism) which also contains genes (xacGHIJK) that encode all components of a putative ABC transporter. The xacGHIJK genes encode one substrate binding protein, two transmembrane domains and two nucleotide binding domains. It is shown here, that xacGHIJK is upregulated by both D-xylose and L-arabinose mediated by the transcriptional regulator XacR, the general regulator of xac genes. Knock-out mutants of xacG and of xacGHIJK resulted in a reduced growth rate on both pentoses; wild type growth could be recovered by complementation in trans. Together, the data indicate that uptake of xylose and arabinose in H. volcanii is mediated by this ABC transporter. Pentose specific ABC transporters, homologous to that of H. volcanii, were identified in other haloarchaea suggesting a similar function in pentose uptake in these archaea. Sequence analyses attribute the haloarchaeal pentose ABC transporter to the CUT1 (carbohydrate uptake transporter 1) subfamily.
The Right Not to be Dominated: The Case Law of the European Court of Human Rights on Migrants’ Destitution
Authors: Slingenberg Lieneke 
Published: April 2019

Abstract
The European Court of Human Rights increasingly deals with migrants’ complaints about destitution in their host state under Article 3 of the European Convention on Human Rights (the prohibition of inhuman and degrading treatment). This case law has been criticized for not being consistent and/or for not providing migrants with enough protection. Based on a systematic case law search, in this article, I analyse Article 3 case law on migrants’ destitution from a new perspective: the concept of freedom as non-domination, as developed in (neo) republican theory. It will argue that, seen through this lens, many tendencies in the Court’s case law can be explained and constructed as consistent, and it is submitted that in this way the Court does provide migrants with important protection against unfreedom. Nevertheless, I also argue in the article that the case law could be improved in a number of ways in order to provide more effective and robust protection against domination.
Morphology, Ecology, and Biogeography of Independent Origins of Cleaning Behavior Around the World
Authors: Baliga Vikram B , Mehta Rita S 
Published: April 2019

AbstractMembers of an ecological guild may be anticipated to show morphological convergence, as similar functional demands exert similar selective pressures on phenotypes. Nature is rife with examples, however, where such taxa instead exhibit ‘incomplete’ convergence or even divergence. Incorporating factors such as character displacement by other guild members or variation in ecological specialization itself may therefore be necessary to gain a more complete understanding of what constrains or promotes diversity. Cleaning, a behavior in which species remove and consume ectoparasites from “clientele,” has been shown to exhibit variation in specialization and has evolved in a variety of marine habitats around the globe. To determine the extent to which specialization in this tropic strategy has affected phenotypic evolution, we examined the evolution of cleaning behavior in five marine fish families: Labridae, Gobiidae, Pomacanthidae, Pomacentridae, and Embiotocidae. We used a comparative framework to determine patterns of convergence and divergence in body shape and size across non-cleaning and cleaning members within these five clades. Highly specialized obligate cleaning, found in the Indo-Pacific and the Caribbean, evolved in the Labridae and Gobiidae at strikingly similar times. In these two regions, obligate cleaning evolves early, shows convergence on an elongate body shape, and is restricted to species of small body size. Facultative cleaning, shown either throughout ontogeny or predominately in the juvenile phase, exhibits a much more varied phenotype, especially in geographic regions where obligate cleaning occurs. Collectively, our results are consistent with varying extents of an ecological specialization constraining or spurring morphological evolution in recurrent ways across regions.
Sharing personal health record data elements in protective custody: youth and stakeholder perspectives
Authors: Dexheimer Judith W , Greiner Mary V , Beal Sarah J , Johnson Darius , Kachelmeyer Andrea , Vaughn Lisa M 
Published: April 2019

AbstractObjectiveThe study sought to develop the necessary elements for a personalized health record (PHR) for youth emancipating from child protective custody (eg, foster care) by collecting thoughts and ideas from current and former foster youth and community stakeholders who have a significant amount of experience working with emancipating young people.Materials and MethodsWe employed a mixed methods, participatory research design using concept mapping to identify key features for PHR across stakeholders.ResultsIn the clusters, common themes for necessary elements for a PHR included health education, health tips, medication instructions, diagnoses including severity, and website resources that could be trusted to provide reliable information, and addressed data privacy issues such as the primary user being able to choose what diagnoses to share with their trusted adult and the ability to assign a trusted adult to view a part of the record.DiscussionBy directly involving youth in the design of the PHR, we are able to ensure we included the necessary health and life skills elements that they require. As a PHR is created for foster youth, it is important to consider the multiple uses that the data may have for emancipated youth.ConclusionA PHR for foster youth needs to include an appropriate combination of information and education for a vulnerable population. In addition to providing some of their basic health and custody information, a PHR provides an opportunity to give them information that can be trusted to explain common diagnoses, medications, and family health history risks.
Total body irradiation induced mouse small intestine senescence as a late effect
Authors: Zhao Yu , Zhang Junling , Han Xiaodan , Fan Saijun 
Published: April 2019

AbstractRadiation can induce senescence in many organs and tissues; however, it is still unclear how radiation stimulates senescence in mouse small intestine. In this study, we use the bone marrow transplantation mouse model to explore the late effects of total body irradiation on small intestine. Our results showed that almost all of the body hairs of the irradiated mice were white (which is an indication of aging) 10 months after the exposure to radiation. Furthermore, compared with the age-matched control mice, there were more SA-β-galactosidase (SA-β-gal)–positive cells and an upregulation of p16 and p21 in 8 Gy–irradiated mice intestinal crypts, indicating that radiation induced senescence in the small intestine. Intestinal bacterial flora profile analysis showed that the diversity of the intestinal bacterial flora decreased in irradiated mice; in addition it showed that the principal components of the irradiated and control mice differed: there was increased abundance of Bacteroidia and a decreased abundance of Clostridia in irradiated mice. To explore the underlying mechanism, an RNA-sequence was executed; the results suggested that pancreatic secretion, and the digestion and absorption of proteins, carbohydrates, fats and vitamins were damaged in irradiated mice, which may be responsible for the body weight loss observed in irradiated mice. In summary, our study suggested that total body irradiation may induce senescence in the small intestine and damage the health status of the irradiated mice.
Estimating Epidemic Incidence and Prevalence from Genomic Data
Authors: Vaughan Timothy G , Leventhal Gabriel E , Rasmussen David A , Drummond Alexei J , Welch David , Stadler Tanja 
Published: April 2019

AbstractModern phylodynamic methods interpret an inferred phylogenetic tree as a partial transmission chain providing information about the dynamic process of transmission and removal (where removal may be due to recovery, death, or behavior change). Birth–death and coalescent processes have been introduced to model the stochastic dynamics of epidemic spread under common epidemiological models such as the SIS and SIR models and are successfully used to infer phylogenetic trees together with transmission (birth) and removal (death) rates. These methods either integrate analytically over past incidence and prevalence to infer rate parameters, and thus cannot explicitly infer past incidence or prevalence, or allow such inference only in the coalescent limit of large population size. Here, we introduce a particle filtering framework to explicitly infer prevalence and incidence trajectories along with phylogenies and epidemiological model parameters from genomic sequences and case count data in a manner consistent with the underlying birth–death model. After demonstrating the accuracy of this method on simulated data, we use it to assess the prevalence through time of the early 2014 Ebola outbreak in Sierra Leone.