bluuebunny/crossref_metadata_2025_split huggingface dataset:
DenVar: density-based variation analysis of multiplex imaging data
Authors: Seal Souvik , Vu Thao , Ghosh Tusharkanti , Wrobel Julia , Ghosh Debashis 
Published: May 2022

AbstractSummaryMultiplex imaging platforms have become popular for studying complex single-cell biology in the tumor microenvironment (TME) of cancer subjects. Studying the intensity of the proteins that regulate important cell-functions becomes extremely crucial for subject-specific assessment of risks. The conventional approach requires selection of two thresholds, one to define the cells of the TME as positive or negative for a particular protein, and the other to classify the subjects based on the proportion of the positive cells. We present a threshold-free approach in which distance between a pair of subjects is computed based on the probability density of the protein in their TMEs. The distance matrix can either be used to classify the subjects into meaningful groups or can directly be used in a kernel machine regression framework for testing association with clinical outcomes. The method gets rid of the subjectivity bias of the thresholding-based approach, enabling easier but interpretable analysis. We analyze a lung cancer dataset, finding the difference in the density of protein HLA-DR to be significantly associated with the overall survival and a triple-negative breast cancer dataset, analyzing the effects of multiple proteins on survival and recurrence. The reliability of our method is demonstrated through extensive simulation studies.Availability and implementationThe associated R package can be found here, https://github.com/sealx017/DenVar.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics
Authors: Privé Florian 
Published: May 2022

AbstractMotivationMeasuring genetic diversity is an important problem because increasing genetic diversity is a key to making new genetic discoveries, while also being a major source of confounding to be aware of in genetics studies.ResultsUsing the UK Biobank data, a prospective cohort study with deep genetic and phenotypic data collected on almost 500 000 individuals from across the UK, we carefully define 21 distinct ancestry groups from all four corners of the world. These ancestry groups can serve as a global reference of worldwide populations, with a handful of applications. Here, we develop a method that uses allele frequencies and principal components derived from these ancestry groups to effectively measure ancestry proportions from allele frequencies of any genetic dataset.Availability and implementationThis method is implemented in function snp_ancestry_summary of R package bigsnpr.Supplementary informationSupplementary data are available at Bioinformatics online.
Automated detection of low ejection fraction from a one-lead electrocardiogram: application of an AI algorithm to an electrocardiogram-enabled Digital Stethoscope
Authors: Attia Zachi I , Dugan Jennifer , Rideout Adam , Maidens John N , Venkatraman Subramaniam , Guo Ling , Noseworthy Peter A , Pellikka Patricia A , Pham Steve L , Kapa Suraj , Friedman Paul A , Lopez-Jimenez Francisco 
Published: May 2022

Abstract

Aims
Electrocardiogram (ECG)-enabled stethoscope (ECG-Scope) acquires a single-lead ECGs during cardiac auscultation and may facilitate real-time screening for pathologies not routinely identified by cardiac auscultation alone. We previously demonstrated an artificial intelligence (AI) algorithm can identify left ventricular dysfunction (LVSD) [defined as ejection fraction (EF) ≤ 40%] with an area under the curve (AUC) of 0.91 using a 12-lead ECG.

Methods and results
One hundred patients referred for clinically indicated echocardiography were prospectively recruited. ECG-Scope recordings with the patient supine and sitting were obtained in multiple electrode locations at the time of the echocardiogram. The AI algorithm for the detection of LVSD was retrained using single leads from ECG-12 and validated against ECG-Scope to determine accuracy for low EF detection (≤35%, &lt;40%, or &lt;50%). We evaluated the algorithm with respect to body position and lead location. Amongst 100 patients (aged 61.3 ± 13.8; 61% male, BMI: 30.0 ± 5.4), eight had EF≤40%, and six had EF 40–50%. The best single recording position was V2 with the patient supine [AUC: 0.88 (CI: 0.80–0.97) for EF≤35%, 0.85 (CI: 0.75–0.95) for EF≤40%, and 0.81 (CI: 0.71–0.90) for EF &lt; 50%]. When using an AI model to select the recording automatically, AUC was 0.91 (CI: 0.84–0.97) for EF≤35%, 0.89 (CI: 0.83–0.96) for EF≤40%, and 0.84 (CI: 0.73–0.94) for EF &lt; 50%.

Conclusion
An AI algorithm applied to an ECG-enabled stethoscope recording in standard auscultation positions reliably detected the presence of a low EF in this prospective study of patients referred for echocardiography. The ability to screen patients with a possible low EF during routine physical examination may facilitate rapid detection of LVSD.
AZI2 positively regulates the induction of type I interferon in influenza-trigger pediatric pneumonia
Authors: Wei Meili , Zheng Yanfei , Xu Jing , Sun Qiwei 
Published: May 2022

Abstract
5-azacytidine-induced protein 2 (AZI2) is known to have a crucial role in antiviral innate immunity. This study aims to explore the roles of AZI2 in influenza-trigger pediatric pneumonia and its molecular mechanism. qPCR and immunoblotting assays were used to determine the levels of target genes and proteins. The lung infection mouse model was established by using PR8 H1N1 virus in AZI2 germline knockout (AZI2−/−) and wild-type (WT) mice. In addition, HEK293T cell-based luciferase reporter assays were used to investigate the regulatory effects of AZI2 on type I interferon. Immune precipitation and immunofluorescence staining were used to evaluate the interactions between AZI2 and TANK binding kinase 1 (TBK1). We observed an elevation in the expressions of IFN-I and AZI2 in peripheral blood mononuclear cells from the pneumonia patients with mild symptoms. Interestingly, AZI2 deficiency deteriorated the influenza-induced pathological symptoms in the lung as well as reduced the survival rate. It was further showed that AZI2 positively regulated the expressions of type I interferon, inflammatory cytokines, and IFN production-related genes. The molecular mechanism data revealed that AZI2 regulated the interactions between TBK1 and TANK. In summary, AZI2 positively regulates type I interferon production in influenza-induced pediatric pneumonia by promoting the interactions between TBK1 and TANK.
Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom
Authors: Snelders Nick C , Rovenich Hanna , Thomma Bart P H J 
Published: May 2022

Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
Male Bowhead Whale Reproductive Histories Inferred from Baleen Testosterone and Stable Isotopes
Authors: Hunt Kathleen E , Buck C Loren , Ferguson Steven H , Fernández Ajo Alejandro , Heide-Jørgensen Mads Peter , Matthews Cory J D 
Published: May 2022

SynopsisMale mammals of seasonally reproducing species typically have annual testosterone (T) cycles, with T usually peaking during the breeding season, but occurrence of such cycles in male mysticete whales has been difficult to confirm. Baleen, a keratinized filter-feeding apparatus of mysticetes, incorporates hormones as it grows, such that a single baleen plate can record years of endocrine history with sufficient temporal resolution to discern seasonal patterns. We analyzed patterns of T every 2 cm across the full length of baleen plates from nine male bowhead whales (Balaena mysticetus) to investigate occurrence and regularity of T cycles and potential inferences about timing of breeding season, sexual maturation, and reproductive senescence. Baleen specimens ranged from 181–330 cm in length, representing an estimated 11 years (smallest whale) to 22 years (largest whale) of continuous baleen growth, as indicated by annual cycles in stable isotopes. All baleen specimens contained regularly spaced areas of high T content (T peaks) confirmed by time series analysis to be cyclic, with periods matching annual stable isotope cycles of the same individuals. In 8 of the 9 whales, T peaks preceded putative summer isotope peaks by a mean of 2.8 months, suggesting a mating season in late winter / early spring. The only exception to this pattern was the smallest and youngest male, which had T peaks synchronous with isotope peaks. This smallest, youngest whale also did not have T peaks in the first half of the plate, suggesting initiation of T cycling during the period of baleen growth. Linear mixed effect models suggest that whale age influences T concentrations, with the two largest and oldest males exhibiting a dramatic decline in T peak concentration across the period of baleen growth. Overall, these patterns are consistent with onset of sexual maturity in younger males and possible reproductive senescence in older males. We conclude that adult male bowheads undergo annual T cycles, and that analyses of T in baleen may enable investigation of reproductive seasonality, timing of the breeding season, and life history of male whales.
Cellular goore game with application to finding maximum clique in social networks
Authors: Khomami Mohammad Mehdi Daliri , Meybodi Mohammad Reza , Ameri Reyhaneh 
Published: May 2022

Abstract
The goore game (GG) is a model for collective decision making under uncertainty, which can be used as a tool for stochastic optimization of a discrete variable function. The GG has a fascinating property that can be resolved in a distributed manner with no intercommunication between the players. The game has found applications in many network applications, including sensor networks, quality-of-service routing, and social networks. In this paper, we introduce an extension of GG called cellular goore game (CGG) for the first time. The CGG is a network of GGs. In this network, each node (or subset of nodes in the network) plays the rule of referees, each of which participates in a GG with its neighboring players (voters) at any time. Like in GG, each player independently selects its optimal action between two available actions based on their gains and losses received from its adjacent referee. Players in CGG know nothing about how other players are playing or even how/why they are rewarded/penalized. The potential of the CGG is shown by providing an algorithm for finding a maximum clique in social networks. Our research provides the first-time study of the CGG for finding a maximum clique in graphs. The performance of the CGG-based algorithm for finding maximum clique is studied on the standard clique benchmark called DIMACS by several experiments. The obtained result shows that the CGG-based algorithm is superior to the existing algorithms in terms of finding maximum clique size and time.
Wee1 kinase inhibitor adavosertib with radiation in newly diagnosed diffuse intrinsic pontine glioma: A Children’s Oncology Group phase I consortium study
Authors: Mueller Sabine , Cooney Tabitha , Yang Xiaodong , Pal Sharmistha , Ermoian Ralph , Gajjar Amar , Liu Xiaowei , Prem Komal , Minard Charles G , Reid Joel M , Nelson Marvin , Haas-Kogan Daphne , Fox Elizabeth , Weigel Brenda J 
Published: May 2022

AbstractBackgroundChildren with diffuse intrinsic pontine gliomas (DIPG) have a dismal prognosis. Adavosertib (AZD1775) is an orally available, blood-brain barrier penetrant, Wee1 kinase inhibitor. Preclinical efficacy against DIPG is heightened by radiation induced replication stress.MethodsUsing a rolling six design, 7 adavosertib dose levels (DLs) (50 mg/m2 alternating weeks, 50 mg/m2 alternating with weeks of every other day, 50 mg/m2, then 95, 130, 160, 200 mg/m2) were assessed. Adavosertib was only given on days of cranial radiation therapy (CRT).The duration of CRT (54 Gy over 30 fractions; 6 weeks) constituted the dose limiting toxicity (DLT) period. Endpoints included tolerability, pharmacokinetics, overall survival (OS) and peripheral blood γH2AX levels as a marker of DNA damage.ResultsA total of 46 eligible patients with newly diagnosed DIPG [median (range) age 6 (3–21) years; 52% female] were enrolled. The recommend phase 2 dose (RP2D) of adavosertib was 200 mg/m2/d during days of CRT. Dose limiting toxicity included ALT elevation (n = 1, DL4) and neutropenia (n = 1, DL7). The mean Tmax, T1/2 and Clp on Day 1 were 2 h, 4.4 h, and 45.2 L/hr/m2, respectively. Modest accumulation of adavosertib was observed comparing day 5 versus day 1 AUC0-8h (accumulation ratio = 1.6). OS was 11.1 months (95% CI: 9.4, 12.5) and did not differ from historical control.ConclusionAdavosertib in combination with CRT is well tolerated in children with newly diagnosed DIPG, however, compared to historical controls, did not improve OS. These results can inform future trial design in children with high-risk cancer.
Dynamic occupancy models reveal Black-billed and Yellow-billed Cuckoos have high rates of turnover during the breeding season
Authors: Johnson Claire A , Benson Thomas J 
Published: May 2022

Abstract
Understanding the conservation needs of rare and hard-to-detect species becomes even more difficult when a species is highly mobile. Black-billed Cuckoos (Coccyzus erythropthalmus) and Yellow-billed Cuckoos (Coccyzus americanus) have experienced extensive range-wide population declines over the last several decades. Low detection probability has made it hard to determine causes of declines and resulted in poorly supported population and trend estimates. However, given evidence that cuckoos make wide-ranging movements during the breeding season, it may be necessary to address issues of both low vocalization rate and availability for detection to better understand these cryptic species. We performed passive and call-broadcast surveys for cuckoos at 41 sites across northern Illinois in 2019 and 2020. We examined the influence of call broadcast and temporal and environmental covariates on detection probability and how habitat covariates affected occupancy, immigration, and emigration both within and among sites. Individual detection probability increased substantially using call broadcasts (12 and 6 times for Black-billed and Yellow-billed Cuckoos, respectively) and detection increased with temperature. Black-billed Cuckoo detection probability also varied temporally, being lowest in the middle of the breeding season. We found strong support for turnover within sites during the breeding season, indicating maintenance of large home ranges, as well as among sites (average emigration probability of 86% and 47% for Black-billed and Yellow-billed Cuckoos, respectively). Black-billed Cuckoos were more likely to use open, shrubby sites and Yellow-billed Cuckoos to use sites with older successional habitat. While turnover rate was affected by habitat covariates, these species’ reliance on ephemeral insect abundance may ultimately be driving occupancy dynamics. Our results suggest that broadcasts are essential for effectively monitoring these cuckoos, but also imply the need to move towards coordinating management at broader spatial scales for these highly mobile species.
Haemosporidian parasite diversity and prevalence in the songbird genusJuncoacross Central and North America
Authors: Martínez-Renau Ester , Rojas-Estévez Natalia , Friis Guillermo , Hernández-Montoya Julio C , Elizondo Pablo , Milá Borja 
Published: May 2022

AbstractThe evolution of host–parasite interactions as host lineages colonize new geographic regions and diversify over evolutionary time is poorly understood. To assess whether haemosporidian parasite diversity has changed during the diversification of an avian host, we surveyed the diversity and prevalence of blood parasite lineages (genera Plasmodium, Haemoproteus, and Leucocytozoon) across the range of the songbird genus Junco, which has diversified recently as it recolonized North America following the last glacial maximum ~18,000 years ago. We report the diversity and prevalence of parasites in junco taxa sampled from Costa Rica to Canada, and examine the influence of local avian species richness in the prevalence and diversity of parasites in junco samples. We screened for parasites in each individual by sequencing a fragment of their cytochrome b gene, identifying the different lineages, and quantifying the prevalence per junco taxon and locality. Of 304 juncos sampled, 178 tested positive for 1 or more parasite genera (58.5% overall prevalence). We found high parasite diversity in genera Haemoproteus and Leucocytozoon and much lower diversity in Plasmodium. Among the 63 parasite lineages detected, 32 of which have not been previously described, we found generalist lineages with widespread but low prevalence in Junco, but also some that appear to have remained specialized on this genus as it diversified across North America over thousands of years. Our results suggest a range of parasitic strategies, ranging from specialized to generalist lineages within single parasite genera.
History and best practices of captive bolt euthanasia for swine
Authors: Anderson Karly N , Deen John , Karczewski Jerry , Zhitnitskiy Perle E , Vogel Kurt D 
Published: May 2022

Abstract
The definition of animal welfare includes how an animal dies. As such, euthanasia is intrinsically linked to animal welfare, and ensuring a good death through effective, safe, and validated practices is a critical piece of promoting positive animal welfare. The objective of this review is to provide a better understanding of the literature on the euthanasia of swine via penetrating captive bolt (PCB) and nonpenetrating captive bolt (NPCB), as well as a history of captive bolt use, and indicators of sensibility and insensibility. To do this, we performed a systematic review that included 30 peer-reviewed articles and 17 other publications. NPCB devices have been validated as an effective single-step euthanasia method for neonatal and preweaning swine, as well as a two-step euthanasia method for nursery swine. PCB devices have been validated as an effective euthanasia method for nursery and market swine up to 120 kg, but further investigation is required for the use of captive bolt devices on mature breeding sows and boars.
Polyclonal antibody preparations from avian origin as a feed additive to beef cattle: ruminal fermentation during the step-up transition diets
Authors: Silva Gleise M , Podversich Federico , Schulmeister Tessa M , Santos Erick R S , Sanford Carla , Siqueira Michelle C B , DiLorenzo Nicolas 
Published: May 2022

Abstract
This study investigated the effects of feeding an avian-derived polyclonal antibody preparation (PAP; CAMAS, Inc.) against Streptococcus bovis, Fusobacterium necrophorum, and lipopolysaccharides (40%, 35%, and 25% of the preparation, respectively) on ruminal fermentation [pH, ammonia-N (NH3-N), lactate, and volatile fatty acids (VFA)] of beef steers during a 21-d step-up diet adaptation. Eight ruminally cannulated Angus crossbred beef steers (658 ± 79 kg of body weight) were assigned in a crossover design to be transitioned from a diet containing ad libitum bermudagrass hay [Cynodon dactylon (L.) Pers.] plus 0.45 kg/d (as fed) of molasses with 0 (CON) or 3 g of PAP (PAP) to a high-grain diet. Transition consisted of three 7-d steps of increased inclusion of cracked corn (35%, 60%, and 82% of the diet DM for STEP1, STEP2, and STEP3, respectively). On each transition day and 7 d after STEP3 (STEP3-7d), ruminal fluid samples were obtained every 3 h for 24 h. Feeding 3 g of PAP daily increased (P &lt; 0.01) average ruminal pH during STEP3 compared with CON steers (5.6 vs. 5.4 ± 0.05, respectively). During STEP1, NH3-N concentration was greater (P &lt; 0.01; 9.4 vs. 6.8 ± 0.74 mM, respectively), and time (min/d) and area (time × pH) of ruminal pH below or equal to 5.2 was lesser (P ≤ 0.03) for steers consuming PAP compared with steers assigned to CON treatment (33.4 vs. 73.3 ± 21.7 min/d and 187.4 vs. 406.3 ± 119.7 min × pH/d, respectively). Steers consuming PAP had greater acetate:propionate ratio at 0, 3, and 6 h relative to diet change compared with CON (2.42, 2.35, 2.29 vs. 1.66, 1.79, and 1.72 ± 0.17, respectively), whereas butyrate molar proportions increased (P = 0.02; 17.1 vs. 11 ± 1.58 mol/100 mol for CON and PAP, respectively) when PAP was not fed at STEP2. Total ruminal lactate concentrations were not affected by PAP feeding (P &gt; 0.11). In conclusion, feeding 3 g/d of polyclonal antibody preparation against S. bovis, F. necrophorum, and lipopolysaccharides was effective in increasing ruminal pH, A:P ratio, and NH3-N concentrations, possibly attenuating the risks of ruminal acidosis in steers during the step-up transition from forage to high-grain diets.