bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limiting factors for milk production in dairy cows: perspectives from physiology and nutrition
Authors: Gross Josef J 
Published: February 2022

Abstract
Milk production in dairy cows increases worldwide since many decades. With rising milk yields, however, potential limiting factors are increasingly discussed. Particularly, the availability of glucose and amino acids is crucial to maintain milk production as well as animal health. Limitations arise from feed sources, the rumen and digestive tract, tissue mobilization, intermediary metabolism and transport, and the uptake of circulating nutrients by the lactating mammary gland. The limiting character can change depending on the stage of lactation. Although physiological boundaries are prevalent throughout the gestation–lactation cycle, limitations are aggravated during the early lactation period when high milk production is accompanied by low feed intake and high mobilization of body reserves. The knowledge about physiological constraints may help to improve animal health and make milk production more sustainably. The scope of this review is to address contemporary factors related to production limits in dairy cows from a physiological perspective. Besides acknowledged physiological constraints, selected environmental and management-related factors affecting animal performance and physiology will be discussed. Potential solutions and strategies to overcome or to alleviate these constraints can only be presented briefly. Instead, they are thought to address existing shortcomings and to identify possibilities for optimization. Despite a scientific-based view on physiological limits, we should keep in mind that only healthy animals could use their genetic capacity and produce high amounts of milk.
Antibiotics Alter the Expression of Genes Related to Behavioral Development in Honey Bees (Hymenoptera: Apidae)
Authors: Ortiz-Alvarado Yarira , Giray Tugrul 
Published: February 2022

Abstract
Honey bees, as many species of social insects, display a division of labor among colony members based on behavioral specializations related to age. Adult worker honey bees perform a series of tasks in the hive when they are young (such as brood care or nursing) and at ca. 2–3 wk of age, shift to foraging for nectar and pollen outside the hive. The transition to foraging involves changes in metabolism and neuroendocrine activities. These changes are associated with a suite of developmental genes. It was recently demonstrated that antibiotics influence behavioral development by accelerating or delaying the onset of foraging depending on timing of antibiotic exposure. To understand the mechanisms of these changes, we conducted a study on the effects of antibiotics on expression of candidate genes known to regulate behavioral development. We demonstrate a delay in the typical changes in gene expression over the lifetime of the individuals that were exposed to antibiotics during immature stage and adulthood. Additionally, we show an acceleration in the typical changes in gene expression on individuals that were expose to antibiotics only during immature stage. These results show that timing of antibiotic exposure alter the typical regulation of behavioral development by metabolic and neuroendocrine processes.
Explaining deep learning of galaxy morphology with saliency mapping
Authors: Bhambra Prabh , Joachimi Benjamin , Lahav Ofer 
Published: February 2022

ABSTRACT
We successfully demonstrate the use of explainable artificial intelligence (XAI) techniques on astronomical data sets in the context of measuring galactic bar lengths. The method consists of training convolutional neural networks on human classified data from Galaxy Zoo in order to predict general galaxy morphologies, and then using SmoothGrad (a saliency mapping technique) to extract the bar for measurement by a bespoke algorithm. We contrast this to another method of using a convolutional neural network to directly predict galaxy bar lengths. These methods achieved correlation coefficients of 0.76 and 0.59, and root mean squared errors of 1.69 and 2.10 respective to human measurements. We conclude that XAI methods outperform conventional deep learning in this case, which could be reasonably explained by the larger data sets available when training the models. We suggest that our XAI method can be used to extract other galactic features (such as the bulge-to-disc ratio) without needing to collect new data sets or train new models. We also suggest that these techniques can be used to refine deep learning models as well as identify and eliminate bias within training data sets.
An observational synthesis of the Taurid meteor complex
Authors: Egal A , Brown P G , Wiegert P , Kipreos Y 
Published: February 2022

ABSTRACTWe provide an overview of the observational properties of the four major Taurid showers, namely the Northern and Southern Taurids (#017 NTA and #002 STA), the β Taurids (#173 BTA), and the ζ Perseids (#172 ZPE). Analysing more than two decades of meteor observations from visual, optical, and radar measurements, we present the Taurids average activity, annual variations in strength, radiant drift, and orbital variations as a function of solar longitude and particle size. The Taurid showers are detected over several weeks in the spring and autumn, but their annual activity level is generally low (less than 15 visual meteors per hour). We find the STA to be pre-dominant in autumn, while its twin, the ZPE, dominates over the BTA in spring. Due to their long duration, the position of each shower’s radiant and orbital elements are variable with time. Optical measurements have previously recorded enhanced STA activity and increased fireball rates caused by the return of a swarm of meteoroids trapped in the 7:2 mean motion resonance with Jupiter. However, we find no presence of the swarm in radar data, suggesting that small meteoroids are removed from the resonance faster than fireball-producing meteoroids. We also find the STA to be enriched in smaller particles early in their activity period. The differences we identify in our analysis between the showers at different particle sizes provide strong observational constraints to future dynamical modelling of the Taurid Meteoroid Complex.
Acceleration and cooling of the corona during X-ray flares from the Seyfert galaxy I Zw 1
Authors: Wilkins D R , Gallo L C , Costantini E , Brandt W N , Blandford R D 
Published: February 2022

ABSTRACTWe report on X-ray flares that were observed from the active galactic nucleus I Zwicky 1 (I Zw 1) in 2020 January by the NuSTAR and XMM-Newton observatories. The X-ray spectrum is well-described by a model comprised of the continuum emission from the corona and its reflection from the accretion disc around a rapidly spinning (a &gt; 0.94) black hole. In order to model the broadband spectrum, it is necessary to account for the variation in ionization across the disc. Analysis of the X-ray spectrum in time periods before, during and after the flares reveals the underlying changes to the corona associated with the flaring. During the flares, the reflection fraction drops significantly, consistent with the acceleration of the corona away from the accretion disc. We find the first evidence that during the X-ray flares, the temperature drops from $140_{-20}^{+100}$ keV before to $45_{-9}^{+40}$ keV during the flares. The profile of the iron K line reveals the emissivity profile of the accretion disc, showing it to be illuminated by a compact corona extending no more than $7_{-2}^{+4}$ rg over the disc before the flares, but with tentative evidence that the corona expands as it is accelerated during the flares. Once the flares subsided, the corona had collapsed to a radius of $6_{-2}^{+2}$ rg. The rapid time-scale of the flares suggests that they arise within the black hole magnetosphere rather than in the accretion disc, and the variation of the corona is consistent with the continuum arising from the Comptonization of seed photons from the disc.
Cdc48Ufd1/Npl4 segregase removes mislocalized centromeric histone H3 variant CENP-A from non-centromeric chromatin
Authors: Ohkuni Kentaro , Gliford Loran , Au Wei-Chun , Suva Evelyn , Kaiser Peter , Basrai Munira A 
Published: February 2022

Abstract
Restricting the localization of CENP-A (Cse4 in Saccharomyces cerevisiae) to centromeres prevents chromosomal instability (CIN). Mislocalization of overexpressed CENP-A to non-centromeric chromatin contributes to CIN in budding and fission yeasts, flies, and humans. Overexpression and mislocalization of CENP-A is observed in cancers and is associated with increased invasiveness. Mechanisms that remove mislocalized CENP-A and target it for degradation have not been defined. Here, we report that Cdc48 and its cofactors Ufd1 and Npl4 facilitate the removal of mislocalized Cse4 from non-centromeric chromatin. Defects in removal of mislocalized Cse4 contribute to lethality of overexpressed Cse4 in cdc48,ufd1 andnpl4 mutants. High levels of polyubiquitinated Cse4 and mislocalization of Cse4 are observed in cdc48-3, ufd1-2 and npl4-1mutants even under normal physiological conditions, thereby defining polyubiquitinated Cse4 as the substrate of the ubiquitin directed segregase Cdc48Ufd1/Npl4. Accordingly, Npl4, the ubiquitin binding receptor, associates with mislocalized Cse4, and this interaction is dependent on Psh1-mediated polyubiquitination of Cse4. In summary, we provide the first evidence for a mechanism that facilitates the removal of polyubiquitinated and mislocalized Cse4 from non-centromeric chromatin. Given the conservation of Cdc48Ufd1/Npl4 in humans, it is likely that defects in such pathways may contribute to CIN in human cancers.
The Burkholderia cenocepacia iron starvation σ factor, OrbS, possesses an on-board iron sensor
Authors: Butt Aaron T , Banyard Christopher D , Haldipurkar Sayali S , Agnoli Kirsty , Mohsin Muslim I , Vitovski Srdjan , Paleja Ameya , Tang Yingzhi , Lomax Rebecca , Ye Fuzhou , Green Jeffrey , Thomas Mark S 
Published: February 2022

Abstract
Burkholderia cenocepacia is an opportunistic pathogen that causes severe infections of the cystic fibrosis (CF) lung. To acquire iron, B. cenocepacia secretes the Fe(III)-binding compound, ornibactin. Genes for synthesis and utilisation of ornibactin are served by the iron starvation (IS) extracytoplasmic function (ECF) σ factor, OrbS. Transcription of orbS is regulated in response to the prevailing iron concentration by the ferric uptake regulator (Fur), such that orbS expression is repressed under iron-sufficient conditions. Here we show that, in addition to Fur-mediated regulation of orbS, the OrbS protein itself responds to intracellular iron availability. Substitution of cysteine residues in the C-terminal region of OrbS diminished the ability to respond to Fe(II) in vivo. Accordingly, whilst Fe(II) impaired transcription from and recognition of OrbS-dependent promoters in vitro by inhibiting the binding of OrbS to core RNA polymerase (RNAP), the cysteine-substituted OrbS variant was less responsive to Fe(II). Thus, the cysteine residues within the C-terminal region of OrbS contribute to an iron-sensing motif that serves as an on-board ‘anti-σ factor’ in the presence of Fe(II). A model to account for the presence two regulators (Fur and OrbS) that respond to the same intracellular Fe(II) signal to control ornibactin synthesis and utilisation is discussed.
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers
Authors: Liu Xiang , Zhao Bo , Shaw Timothy I , Fridley Brooke L , Duckett Derek R , Tan Aik Choon , Teng Mingxiang 
Published: February 2022

Abstract
Super enhancers (SEs) are broad enhancer domains usually containing multiple constituent enhancers that hold elevated activities in gene regulation. Disruption in one or more constituent enhancers causes aberrant SE activities that lead to gene dysregulation in diseases. To quantify SE aberrations, differential analysis is performed to compare SE activities between cell conditions. The state-of-art strategy in estimating differential SEs relies on overall activities and neglect the changes in length and structure of SEs. Here, we propose a novel computational method to identify differential SEs by weighting the combinatorial effects of constituent-enhancer activities and locations (i.e. internal dynamics). In addition to overall activity changes, our method identified four novel classes of differential SEs with distinct enhancer structural alterations. We demonstrate that these structure alterations hold distinct regulatory impact, such as regulating different number of genes and modulating gene expression with different strengths, highlighting the differentiated regulatory roles of these unexplored SE features. When compared to the existing method, our method showed improved identification of differential SEs that were linked to better discernment of cell-type-specific SE activity and functional interpretation.
Isolated Pulmonary Emergomycosis in an Immunocompetent Patient in Alberta, Canada
Authors: Mah Jordan , Bakker Andrea , Tseng Calvin , Lafay-Cousin Lucie , Kuhn Susan , Brundler Marie-Anne , Lisboa Luiz F 
Published: February 2022

Abstract
Emergomyces canadensis pulmonary infection was incidentally diagnosed in an asymptomatic patient suspected to have metastatic osteosarcoma. Molecular diagnosis was imperative to fungal identification given overlapping histopathological features with histoplasmosis. This report documents a case of isolated pulmonary emergomycosis in an otherwise immunocompetent patient while discussing diagnostic and management pitfalls of this emerging and underdiagnosed infection.
Efficacy of Noncarbapenem β-Lactams Compared to Carbapenems for Extended-Spectrum β-Lactamase–Producing Enterobacterales Urinary Tract Infections
Authors: Anderson Daniel T , Albrecht Benjamin , Jones K Ashley , Jacob Jesse T , Sexton Mary Elizabeth , Wiley Zanthia , Dube William C , Lee Benjamin , Suchindran Sujit 
Published: February 2022

Abstract

Background
Extended-spectrum β-lactamase (ESBL)–producing Enterobacterales are frequent causes of urinary tract infections (UTIs). Severe infections caused by ESBL Enterobacterales are often treated with carbapenems, but optimal treatment for less severe infections such as UTIs is unclear.

Methods
This retrospective cohort study included patients admitted to 4 hospitals in an academic healthcare system with an ESBL UTI treated with either a noncarbapenem β-lactam (NCBL) or a carbapenem for at least 48 hours from 1 April 2014 to 30 April 2018. Those who received an NCBL were compared to those receiving a carbapenem, with a primary outcome of hospital length of stay (LOS) and secondary outcomes of clinical and microbiological response, days until transition to oral therapy, rate of relapsed infection, and rate of secondary infections with a multidrug-resistant organism.

Results
Characteristics were similar among patients who received carbapenems (n = 321) and NCBLs (n = 171). There was no difference in LOS for the NCBL group compared to the carbapenem group (13 days vs 15 days, P = .66). The NCBL group had higher rates of microbiologic eradication (98% vs 92%, P = .002), shorter time to transition to oral therapy (5 days vs 9 days, P &lt; .001), shorter overall durations of therapy (7 days vs 10 days, P &lt; .001), and lower rates of relapsed infections (5% vs 42%, P = .0003).

Conclusions
Patients treated with NCBLs had similar LOS, higher rates of culture clearance, and shorter durations of antibiotic therapy compared to patients treated with carbapenems, suggesting that treatment for ESBL UTIs should not be selected solely based on phenotypic resistance.
Costs and Prescribing Patterns of Anthelmintics in the United States Military: A Retrospective Analysis
Authors: Lindrose Alyssa R , Fraser Jamie A , Hickey Patrick W , Mitre Edward 
Published: February 2022

Abstract

Background
Recent price increases in medications used to treat helminth infections have had demonstrated impacts on Medicaid and immigrant patient populations. Helminth infections are common within the US military; however, anthelmintic prescribing patterns and costs have not yet been investigated in this patient population.

Methods
We conducted a retrospective analysis of pharmaceutical data from the Military Health System Data Repository between fiscal years 2012 and 2019. Prescription information, including costs and demographics, were abstracted for all anthelmintic medications as well as associated helminth diagnostic codes within 30 days of the prescription dispensing date.

Results
On average, there were 10 871 anthelmintic medications prescribed per year, for a total of 86 697 during the study period. Ivermectin and albendazole were each prescribed &gt;34 000 times. There were 15 498 mebendazole prescriptions and 1327 praziquantel prescriptions. The total cost of all anthelmintic prescriptions was $16 018 381. Annual costs for anthelmintic medications increased 16-fold during the study period, up to nearly $5 000 000 in fiscal year 2019, primarily driven by price increases in albendazole and mebendazole. Albendazole prescriptions accounted for $12 282 891 of total costs (76.7%), though only 39.1% of total prescriptions. The most common diagnosis associated with albendazole and mebendazole prescriptions was enterobiasis.

Conclusions
Price increases in anthelmintic medications have significantly impacted the costs borne by the US government for treating parasitic infections. There are a substantial number of anthelmintic prescriptions in the US military health care system annually, suggesting a higher number of helminth infections than previously thought.
IL-25 participates in keratinocyte-driven dermal matrix turnover and is reduced in systemic sclerosis epidermis
Authors: Russo Barbara , Borowczyk Julia , Cacialli Pietro , Moguelet Philippe , Truchetet Marie-Elise , Modarressi Ali , Brembilla Nicolò C , Bertrand Julien , Boehncke Wolf-Henning , Chizzolini Carlo 
Published: February 2022

Abstract

Objectives
Evidence shows that dysfunctional SSc keratinocytes contribute to fibrosis by altering dermal homeostasis. Whether IL-25, an IL-17 family member regulating many epidermal functions, takes part in skin fibrosis is unknown. Here we address the role of IL-25 in skin fibrosis.

Methods
The expression of IL-25 was evaluated by immunofluorescence and in situ hybridization in 10 SSc and seven healthy donor (HD) skin biopsies. Epidermal equivalents (EE) reconstituted by primary HD keratinocytes were used as a model to study transcriptomic changes induced by IL-25 in the epidermis. RNA expression profile in EEs was characterized by RNAseq. The conditioned medium (CM) from primary SSc and HD keratinocytes primed with IL-25 was used to stimulate fibroblasts. IL-6, IL-8, MMP-1, type-I collagen (Col-I), and fibronectin production by fibroblasts was assessed by ELISA.

Results
SSc epidermis expressed lower levels of IL-25 compared with HDs. In EEs, IL-25 regulated several molecular pathways related to wound healing and extracellular matrix remodelling. Compared with control CM, the CM from IL-25-primed keratinocytes enhanced the fibroblast production of MMP-1, IL-6 and IL-8, but not of Col-I nor fibronectin. However, IL-25 significantly reduced the production of Col-I when applied directly to fibroblasts. The activation of keratinocytes by IL-25 was receptor-dependent and evident after a very short incubation time (10 min), largely mediated by IL-1, suggesting enhanced and specific release of preformed mediators.

Conclusions
These results show that IL-25 participates in skin homeostasis, and its decreased expression in SSc may contribute to skin fibrosis by favouring extracellular matrix deposition over degradation.
Dioxin Disrupts Thyroid Hormone and Glucocorticoid Induction of klf9, a Master Regulator of Frog Metamorphosis
Authors: Han David T , Zhao Weichen , Powell Wade H 
Published: February 2022

Abstract
Frog metamorphosis, the development of an air-breathing froglet from an aquatic tadpole, is controlled by thyroid hormone (TH) and glucocorticoids (GC). Metamorphosis is susceptible to disruption by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AHR) agonist. Krüppel-like factor 9 (klf9), an immediate early gene in the endocrine-controlled cascade of expression changes governing metamorphosis, can be synergistically induced by both hormones. This process is mediated by an upstream enhancer cluster, the klf9 synergy module (KSM). klf9 is also an AHR target. We measured klf9 mRNA following exposures to triiodothyronine (T3), corticosterone (CORT), and TCDD in the Xenopus laevis cell line XLK-WG. klf9 was induced 6-fold by 50 nM T3, 4-fold by 100 nM CORT, and 3-fold by 175 nM TCDD. Cotreatments of CORT and TCDD or T3 and TCDD induced klf9 7- and 11-fold, respectively, whereas treatment with all 3 agents induced a 15-fold increase. Transactivation assays examined enhancers from the Xenopus tropicalis klf9 upstream region. KSM-containing segments mediated a strong T3 response and a larger T3/CORT response, whereas induction by TCDD was mediated by a region ∼1 kb farther upstream containing 5 AHR response elements (AHREs). This region also supported a CORT response in the absence of readily identifiable GC responsive elements, suggesting mediation by protein-protein interactions. A functional AHRE cluster is positionally conserved in the human genome, and klf9 was induced by TCDD and TH in HepG2 cells. These results indicate that AHR binding to upstream AHREs represents an early key event in TCDD’s disruption of endocrine-regulated klf9 expression and metamorphosis.
Genetic Diversity of Phymatotrichopsis omnivora Based on Mating Type and Microsatellite Markers Reveals Heterothallic Mating System
Authors: Mattupalli Chakradhar , Cuenca Fernanda Proaño , Shiller Jason B. , Watkins Tara , Hansen Karen , Garzon Carla D. , Marek Stephen M. , Young Carolyn A. 
Published: February 2022

Phymatotrichopsis omnivora is a member of Pezizomycetes and causes root rot disease on a broad range of dicotyledonous plants. Using recently generated draft genome sequence data from four P. omnivora isolates, we developed simple sequence repeat (SSR) markers and identified both mating type genes (MAT1-1-1 and MAT1-2-1) in this fungus. To understand the genetic diversity of P. omnivora isolates (n = 43) and spore mats (n = 29) collected from four locations (Oklahoma, Texas, Arizona, and Mexico) and four host crops (cotton, alfalfa, peach, and soybean), we applied 24 SSR markers and showed that of the 72 P. omnivora isolates and spore mats tested, 41 were distinct genotypes. Furthermore, the developed SSR markers did not show cross-transferability to other close relatives of P. omnivora in the class Pezizomycetes. A multiplex PCR detecting both mating type idiomorphs and a reference gene (TUB2) was developed to screen P. omnivora isolates. Based on the dataset we tested, P. omnivora is a heterothallic fungus with both mating types present in the United States in a ratio close to 1:1. We tested P. omnivora spore mats obtained from spatially distinct disease rings that developed in a center-pivot alfalfa field and showed that both mating types can be present not only in the same field but also within a single spore mat. This study shows that P. omnivora has the genetic toolkit for generating sexually diverse progeny, providing impetus for future studies that focus on identifying sexual morphs in nature.