bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-Prism 2.0: Enabling algorithm and web server for ultra-fast, memory-efficient, and accurate analysis among millions of microbial community samples
Authors: Kang Kai , Chong Hui , Ning Kang 
Published: July 2022

Abstract

Background
Microbial community samples have been accumulating at a speed faster than ever, with hundreds of thousands of samples been sequenced each year. Mining such a huge amount of multisource heterogeneous data is becoming an increasingly difficult challenge, so efficient and accurate compare and search of samples is in urgent need: faced with millions of samples in the data repository, traditional sample comparison and search approaches fall short in speed and accuracy.

Findings
Here we proposed Meta-Prism 2.0, a microbial community sample analysis method that has pushed the time and memory efficiency to a new limit without compromising accuracy. Based on sparse data structure, time-saving instruction pipeline, and SIMD optimization, Meta-Prism 2.0 has enabled ultra-fast, memory-efficient, flexible, and accurate search among millions of samples. Meta-Prism 2.0 was put to test on several data sets, with the largest containing 1 million samples. Results show that Meta-Prism 2.0’s 0.00001-s per sample pair compare speed and 8-GB memory needs for searching against 1 million samples have made it one of the most efficient sample analysis methods. Additionally, Meta-Prism 2.0 can achieve accuracy comparable with or better than other contemporary methods. Third, Meta-Prism 2.0 can precisely identify the original biome for samples, thus enabling sample source tracking. Finally, we have provided a web server for fast search of microbial community samples online.

Conclusions
In summary, Meta-Prism 2.0 has changed the resource-intensive sample search scheme to an effective procedure, which could be conducted by researchers every day even on a laptop, for insightful sample search, similarity analysis, and knowledge discovery. Meta-Prism 2.0 can be accessed at https://github.com/HUST-NingKang-Lab/Meta-Prism-2.0, and the web server can be accessed at https://hust-ningkang-lab.github.io/Meta-Prism-2.0/.
Functional Morphology of the Urohyal Shunt for Symmetrical and Asymmetrical Ventilation in the Flatfish, Isopsetta isolepis
Authors: Amacker K , Farina S C 
Published: July 2022

Abstract
Flatfishes are benthic fishes that are well known for their ability to bury in the sediment, making the transition from above to below the sediment in a matter of seconds. Laterally flattened bodies allow flatfishes to lay flush against the substrate, a behavior facilitated by having an asymmetrical neurocranium with two eyes on one side of the head. Despite neurocranial asymmetry, their gill chambers are highly symmetrical. Additionally, most flatfishes have a uniquely shaped urohyal bone that forms passageway for water to travel ventrally between the “eyed-side” and “blind-side” gill chambers. Our study examines whether the kinematics and pressures generated by the gill chambers are also symmetrical during breathing above and below the sediment and during rapid burial in sediment. We studied Isopsetta isolepis individuals using sonomicrometry crystals to measure the changes in positions of the opercle bones relative to the urohyal and pressure transducers to record gill chamber pressures during burial. We conclude I. isolepis exhibit both symmetrical and asymmetrical breathing above and below the sediment. Pressures and movements were highly asymmetrical during burial jetting. We observed motions that indicate that the urohyal is an active shunt to allow passage of water between the eyed to the blind-side gill chambers.
CD8 T-cell heterogeneity during T-cell exhaustion and PD-1-targeted immunotherapy
Authors: Ando Satomi , Araki Koichi 
Published: July 2022

Abstract
Persistent antigenic stimulation results in loss of effector function or physical deletion of antigen-specific CD8 T cells. This T-cell state is called T-cell exhaustion and occurs during chronic infection and cancer. Antigen-specific CD8 T cells during T-cell exhaustion express the inhibitory receptor PD-1, the expression of which plays a major role in T-cell dysfunction. PD-1 blockade re-invigorates CD8 T-cell immunity and has been proven effective against many different types of human cancer. To further improve the efficacy of PD-1-targeted immunotherapy in cancer patients, a better understanding of T-cell exhaustion is required. Recent studies have revealed that antigen-specific CD8 T cells during T-cell exhaustion are heterogeneous and have also uncovered the detailed mechanisms for PD-1-targeted immunotherapy. Here, we review the CD8 T-cell subsets that arise during T-cell exhaustion, the lineage relationship among these individual subsets and the role of each subset in PD-1 blockade. Also, we discuss potential strategies to enhance the efficacy of PD-1-targeted immunotherapy.
Masculinized Sexual Ornaments in Female Lizards Correlate with Ornament-Enhancing Thermoregulatory Behavior
Authors: Assis B A , Avery J D , Earley R L , Langkilde T 
Published: July 2022

Synopsis
The adaptive significance of colorful or exaggerated traits (i.e., ornaments) expressed in females is often unclear. Competing hypotheses suggest that expression of female ornaments arises from maladaptive (or neutral) genetic inheritance from males along with incomplete epigenetic regulation, or from positive selection for ornaments in females under social competition. Whether costly or advantageous, the visibility of such traits can sometimes be behaviorally modulated in order to maximize fitness. Female eastern fence lizards express blue badges that are variable in size and color saturation. These are rudimentary compared to those seen in males and carry important costs such as reduced mating opportunities. Body temperature is a well-established enhancer of badge color, and thus thermoregulation may be one way these animals modulate badge visibility. We quantified realized body temperatures of female lizards paired in laboratory trials and observed that females with larger badges attained higher body temperatures when freely allowed to thermoregulate, sometimes beyond physiological optima. In this association between phenotype and behavior, females with larger badges exhibited thermoregulatory patterns that increase their badges’ visibility. This signal-enhancing behavior is difficult to reconcile with the widely held view that female ornaments are maladaptive, suggesting they may carry context-dependent social benefits.
A scoping review of ethics considerations in clinical natural language processing
Authors: Bear Don’t Walk Oliver J , Reyes Nieva Harry , Lee Sandra Soo-Jin , Elhadad Noémie 
Published: July 2022

Abstract

Objectives
To review through an ethics lens the state of research in clinical natural language processing (NLP) for the study of bias and fairness, and to identify gaps in research.

Methods
We queried PubMed and Google Scholar for articles published between 2015 and 2021 concerning clinical NLP, bias, and fairness. We analyzed articles using a framework that combines the machine learning (ML) development process (ie, design, data, algorithm, and critique) and bioethical concepts of beneficence, nonmaleficence, autonomy, justice, as well as explicability. Our approach further differentiated between biases of clinical text (eg, systemic or personal biases in clinical documentation towards patients) and biases in NLP applications.

Results
Out of 1162 articles screened, 22 met criteria for full text review. We categorized articles based on the design (N = 2), data (N = 12), algorithm (N = 14), and critique (N = 17) phases of the ML development process.

Discussion
Clinical NLP can be used to study bias in applications reliant on clinical text data as well as explore biases in the healthcare setting. We identify 3 areas of active research that require unique ethical considerations about the potential for clinical NLP to address and/or perpetuate bias: (1) selecting metrics that interrogate bias in models; (2) opportunities and risks of identifying sensitive patient attributes; and (3) best practices in reconciling individual autonomy, leveraging patient data, and inferring and manipulating sensitive information of subgroups. Finally, we address the limitations of current ethical frameworks to fully address concerns of justice. Clinical NLP is a rapidly advancing field, and assessing current approaches against ethical considerations can help the discipline use clinical NLP to explore both healthcare biases and equitable NLP applications.
Amphetamines in Workplace Testing Hair Samples over the Years 2011–2020
Authors: Hill Virginia A , Schaffer Michael I , Paulsen Ryan B , Stowe G Neil 
Published: July 2022

AbstractAmphetamines (AMPs) in hair were investigated with thousands of workplace testing head and body hair samples collected and analyzed over 10 years and tabulated by year. All samples were washed by a published extensive method prior to confirmation by liquid chromatography–mass spectrometry-mass spectrometry. Presented are concentrations of parent methamphetamine (METH), 3,4-methylenedioxymethamphetamine (MDMA) and methylenedioxyamphetamine as metabolite and AMP as metabolite and without the presence of parent drug. Some differences in METH concentrations from year to year were significant, and some ratios of metabolite to parent drug for both METH and MDMA also varied significantly. While rates of METH use may not have changed significantly, some aspects of the drugs ingested as demonstrated by hair analysis varied over the 10-year period.
Introduction to the Collection: Climate Change, Insect Pests, and Beneficial Arthropods in Production Systems
Authors: Eigenbrode Sanford D , Adhikari Subodh , Kistner-Thomas Erica , Neven Lisa 
Published: July 2022

AbstractClimate change is expected to alter pressure from insect pests and the abundance and effectiveness of insect pollinators across diverse agriculture and forestry systems. In response to warming, insects are undergoing or are projected to undergo shifts in their geographic ranges, voltinism, abundance, and phenology. Drivers include direct effects on the focal insects and indirect effects mediated by their interactions with species at higher or lower trophic levels. These climate-driven effects are complex and variable, sometimes increasing pest pressure or reducing pollination and sometimes with opposite effects depending on climatic baseline conditions and the interplay of these drivers. This special collection includes several papers illustrative of these biological effects on pests and pollinators. In addition, in response to or anticipating climate change, producers are modifying production systems by introducing more or different crops into rotations or as cover crops or intercrops or changing crop varieties, with potentially substantial effects on associated insect communities, an aspect of climate change that is relatively understudied. This collection includes several papers illustrating these indirect production system-level effects. Together, biological and management-related effects on insects comprise the necessary scope for anticipating and responding to the effects of climate change on insects in agriculture and forest systems.
Preliminary Study on Comparative Efficacy of Four Light Sources for Trapping Culicoides spp. (Diptera: Ceratopogonidae) in Prachuap Khiri Khan Province, Thailand
Authors: Choocherd Suchada , Pattanatanang Khampee , Chimnoi Wissanuwat , Kamyingkird Ketsarin , Tongyoo Pumipat , Phasuk Jumnongjit 
Published: July 2022

Abstract
The light trap is an important tool to determine the presence and abundance of vectors in the field. However, no one has studied the efficiency of light traps for collecting Culicoides in Thailand. In the present study, the efficacy of four light sources was evaluated in Prachuap Khiri Khan province, Thailand. Incandescent (INCND) light, white fluorescent (WHT-FLR) light, ultraviolet fluorescent (UV-FLR) light, and UV light-emitting diode (UV-LED) light were tested using commercial traps. In total, 30,866 individuals of Culicoides species were collected from November 2020 to June 2021, of which 21,016 were trapped on site 1 and 6,731 were trapped on site 2. The two most abundant Culicoides species were C. imicola (54%) and C. oxystoma (31.2%). UV-FLR was highly effective, followed by UV-LED light, WHT-FLR light, and INCND light, respectively, for Culicoides collection. Significantly, more Culicoides species were collected in those traps baited with UV-FLR light, UV-LED light, or WHT-FLR light than for INCND light traps. Traps equipped with UV-FLR lights can be recommended to trap Culcoides biting midges for monitoring purposes.
Refiguring Slavery Through International Law: The 1926 Slavery Convention, the ‘Native Labor Code’ and Racial Capitalism
Authors: Gevers Christopher 
Published: July 2022

ABSTRACT
This article charts the refiguration of slavery through international law, the concatenations of slavery, colonialism and their afterlives in the present, and what these might tell us about racial capitalism and international economic law. Drawing on the Black Radical Tradition, it shows how slavery was refigured in two distinct but related respects. First, from the late nineteenth century onwards, international lawyers ‘refigured’ slavery historically, such that ‘antislavery’ became a defining attribute of ‘progressive’, ‘white’, ‘civilization’, and set about building the international legal architecture to confirm this fabrication; culminating in the Slavery Convention (1926) and the League of Nations’ ‘antislavery’ machinery. As a result, as a matter of ‘history’ and international law, the ‘recrudescence’ of slavery could only take place in Africa, and in particular in the two African states not yet under white rule—Liberia and Ethiopia—which laid the basis for the violent interventions in these Black Republics by Italy and the League in the interwar period. Second, the Slavery Convention and the International Labor Organization’s ‘native labor code’—through the figure of the ‘Black Worker’—refigured the afterlives of slavery and colonialism as acceptable, ‘civilizing’ (forced) labor, provided it was under white management. The article ends by showing how white supremacy and Black subordination were refigured, materially and symbolically—at both the international and individual level—through the ‘fabulation of debt’, literal and moral; and, in turn, surfaces slavery and colonialism’s entwined afterlives in the racial capitalist present, including through interntational (economic) law.
Helicobia neuzalmeidae sp. nov., A New Species of Sarcophagidae (Diptera) Reared From a Pig Carcass in the Brazilian Savanna
Authors: Silva José Orlando A , Brasil Leandro S , De-Souza Caroline C , Carvalho-Filho Fernando S 
Published: July 2022

Abstract
A new species of Sarcophagidae (Diptera) in the genus Helicobia Coquillett, Helicobia neuzalmeidae sp. nov., is described based on two male specimens obtained from pig carcasses in savanna-like vegetation in northeastern Brazil (state of Maranhão) during a forensic study. The holotype was obtained from a larva that abandoned the pig carcass to pupate, whereas the paratype was collected with a trap placed above the cage containing the carcass. This is the first record of a Helicobia species reared from a vertebrate carcass.
The Location of Disease-Causing DES Variants Determines the Severity of Phenotype and the Morphology of Sarcoplasmic Aggregates
Authors: Silva André Macedo Serafim , Rodrigo Patricia , Moreno Cristiane Araújo Martins , Mendonça Rodrigo de Holanda , Estephan Eduardo de Paula , Camelo Clara Gontijo , Campos Eliene Dutra , Dias Alexandre Torchio , Nascimento Amom Mendes , Kulikowski Leslie Domenici , Oliveira Acary Souza Bulle , Reed Umbertina Conti , Goldfarb Lev G , Olivé Montse , Zanoteli Edmar 
Published: July 2022

Abstract
Desmin (DES) is the main intermediate muscle filament that connects myofibrils individually and with the nucleus, sarcolemma, and organelles. Pathogenic variants of DES cause desminopathy, a disorder affecting the heart and skeletal muscles. We aimed to analyze the clinical features, morphology, and distribution of desmin aggregates in skeletal muscle biopsies of patients with desminopathy and to correlate these findings with the type and location of disease-causing DES variants. This retrospective study included 30 patients from 20 families with molecularly confirmed desminopathy from 2 neuromuscular referral centers. We identified 2 distinct patterns of desmin aggregates: well-demarcated subsarcolemmal aggregates and diffuse aggregates with poorly delimited borders. Pathogenic variants located in the 1B segment and the tail domain of the desmin molecule are more likely to present with early-onset cardiomyopathy compared to patients with variants in other segments. All patients with mutations in the 1B segment had well-demarcated subsarcolemmal aggregates, but none of the patients with variants in other desmin segments showed such histological features. We suggest that variants located in the 1B segment lead to well-shaped subsarcolemmal desmin aggregation and cause disease with more frequent cardiac manifestations. These findings will facilitate early identification of patients with potentially severe cardiac syndromes.
Impact of national lockdown on the suspected SARS-CoV-2 epidemic in terms of the number of fever cases in North Korea
Authors: Han Changhee , Ryu Sukhyun , Shin Hyewon , Kim Dasom , Modchang Charin 
Published: July 2022

After reopening the border, North Korea was experiencing community transmission of SARS-CoV-2 and implemented a nationwide lockdown. We estimated that the mean transmissibility declined to &lt;1 within 5 days after the lockdown and that the lockdown was associated with a moderate decrease in transmissibility by 11% (95% confidence interval, 6–17%).
Abundance stratification in Type Ia supernovae – VI. The peculiar slow decliner SN 1999aa
Authors: Aouad Charles J , Mazzali Paolo A , Hachinger Stephan , Teffs Jacob , Pian Elena , Ashall Chris , Benetti Stefano , Filippenko Alexei V , Tanaka Masaomi 
Published: July 2022

ABSTRACT
The abundance distribution in the ejecta of the peculiar slowly declining Type Ia supernova (SN Ia) SN 1999aa is obtained by modelling a time series of optical spectra. Similar to SN 1991T, SN 1999aa was characterized by early-time spectra dominated by Fe iii features and a weak Si ii 6355 Å line, but it exhibited a high-velocity Ca ii H&K line and morphed into a spectroscopically normal SN Ia earlier. Three explosion models are investigated, yielding comparable fits. The innermost layers are dominated by ∼0.3 M⊙ of neutron-rich stable iron-group elements, mostly stable iron. Above that central region lies a 56Ni-dominated shell, extending to $v \approx 11\, 000$–$12\, 000$ km s−1, with mass ∼0.65 M⊙. These inner layers are therefore similar to those of normal SNe Ia. However, the outer layers exhibit composition peculiarities similar to those of SN 1991T: The intermediate-mass elements shell is very thin, containing only ∼0.2 M⊙, and is sharply separated from an outer oxygen-dominated shell, which includes ∼0.22 M⊙. These results imply that burning suddenly stopped in SN 1999aa. This is a feature SN 1999aa shares with SN 1991T, and explains the peculiarities of both SNe, which are quite similar in nature apart from the different luminosities. The spectroscopic path from normal to SN 1991T-like SNe Ia cannot be explained solely by a temperature sequence. It also involves composition layering differences, suggesting variations in the progenitor density structure or in the explosion parameters.
An orbital perspective on the starvation, stripping, and quenching of satellite galaxies in the eagle simulations
Authors: Wright Ruby J , Lagos Claudia del P , Power Chris , Stevens Adam R H , Cortese Luca , Poulton Rhys J J 
Published: July 2022

ABSTRACT
Using the eagle (Evolution and Assembly of GaLaxies and their Environments) suite of simulations, we demonstrate that both cold gas stripping and starvation of gas inflow play an important role in quenching satellite galaxies across a range of stellar and halo masses, M⋆ and M200. Quantifying the balance between gas inflows, outflows, and star formation rates, we show that even at z = 2, only $\approx 30{{\ \rm per\ cent}}$ of satellite galaxies are able to maintain equilibrium or grow their reservoir of cool gas – compared to $\approx 50{{\ \rm per\ cent}}$ of central galaxies at this redshift. We find that the number of orbits completed by a satellite on first-infall to a group environment is a very good predictor of its quenching, even more so than the time since infall. On average, we show that intermediate-mass satellites with M⋆ between will be quenched at $10^{9}\, {\rm M}_{\odot }\, {\rm and}\, 10^{10}\, {\rm M}_{\odot }$ first pericenter in massive group environments, $M_{200}\gt 10^{13.5}\, {\rm M}_{\odot }$; and will be quenched at second pericenter in less massive group environments, $M_{200}\lt 10^{13.5}\, {\rm M}_{\odot }$. On average, more massive satellites ($M_{\star }\gt 10^{10}\, {\rm M}_{\odot }$) experience longer depletion time-scales, being quenched between first and second pericenters in massive groups, while in smaller group environments, just $\approx 30{{\ \rm per\ cent}}$ will be quenched even after two orbits. Our results suggest that while starvation alone may be enough to slowly quench satellite galaxies, direct gas stripping, particularly at pericenters, is required to produce the short quenching time-scales exhibited in the simulation.
Extreme blazars: the result of unstable recollimated jets?
Authors: Tavecchio Fabrizio , Costa Agnese , Sciaccaluga Alberto 
Published: July 2022

ABSTRACT
Extreme BL Lacs (EHBL) form a subclass of blazars, which challenge standard emission scenarios. In a recent study it has been argued that their peculiar properties can be explained if emitting electrons are accelerated in a series of oblique shocks induced by the recollimation of the relativistic jet. However, new 3 D simulations of recollimated, weakly magnetized jets reveal that, in correspondence with the first recollimation shock, the flow develops a rapidly growing instability, becomes highly turbulent and decelerates, effectively hampering the formation of the multiple shock structure routinely observed in 2 D simulations. Building on these new findings, we propose here a revised scenario for EHBL, in which the emission is produced by electrons accelerated at the recollimation shock and subsequently further energized through stochastic acceleration in the turbulent downstream flow. We apply a simple version of this scenario to the prototypical EHBL 1ES 0229-200, showing that the spectral energy distribution (SED) can be satisfactorily reproduced with standard values of the main physical parameters.