bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of restricting energy during the gilt development period on growth and reproduction of lines differing in lean growth rate: responses in reproductive performance and longevity
Authors: Johnson Rodger K , Trenhaile-Grannemann Melanie D , Moreno Roman , Ciobanu Daniel C , Miller Phillip S 
Published: December 2021

AbstractLongevity and reproductive performance are economically important traits in the swine industry that are largely influenced by nutrition and other environmental factors. Reproductive performance and longevity through 4 parities was assessed in gilts of 2 genetic lines developed on ad libitum access to feed or restricted to 75% of ad libitum intake. A total of 661 gilts were used in a 2 × 2 factorial with half of the gilts allocated to an ad libitum diet (AL; n = 330), while the other half were energy restricted by 25% (R; n = 331) from 123 to 235 d of age. All gilts were sired by an industry maternal line. Dams of the gilts were from either a Large White (W) by Landrace (L) industry maternal line or Nebraska Selection Line 45X, producing gilts designated as W × L (n = 355) and L45X (n = 306), respectively. Daily estrus detection began at 140 d of age to obtain age at puberty (AP). Gilts (n = 510) were mated on their second or later estrus, beginning at 240 d of age. Sow weight and backfat were recorded at 110 d of gestation and weaning of each parity. Number of live-born, stillborn, and mummified pigs per litter and piglet birth and weaning weights were recorded through 4 parities. More L45X than W × L and more AL than R gilts reached puberty by 230 d of age (P &lt; 0.01). Dietary treatment did not affect probability to produce parities 1 to 4 or any litter trait analyzed. The L45X females tended to be more likely to produce parities 1 (P &lt; 0.08) and 3 (P &lt; 0.06), while W × L had heavier litters at birth (P &lt; 0.01) and weaning (P = 0.01). Treatment by parity interactions (P &lt; 0.01) existed for weight and backfat prior to farrowing and backfat at weaning, and weight at weaning exhibited a line by treatment by parity interaction (P = 0.04) as R sows had lower weights and backfats in earlier parities, but caught up to AL sows in later parities. A treatment by parity interaction (P &lt; 0.01) was also present for backfat loss from farrowing to weaning as R gilts lost less backfat than AL in parities 1 and 2, but more in parities 3 and 4. No significant differences were detected between lines or treatments for lifetime production traits. The populations of pigs and data presented here provide a framework for a diverse array of further studies. Alternative approaches to restrict energy have been assessed in addition to methods of marker-assisted and genomic selection for improvement of litter size and sow longevity.
Postglacial colonization in the Great Lakes Region by the white-footed mouse (Peromyscus leucopus): conflicts between genomic and field data
Authors: Prado Joyce R , Rubi Tricia L , Baumgartner Joseph , Hoffman Susan M G , Dantzer Ben , Lacey Knowles L 
Published: December 2021

Abstract
For regions that were covered by ice during the Pleistocene glaciations, species must have emigrated from unglaciated regions. However, it can be difficult to discern when and from what ancestral source populations such expansions took place, especially since warming climates introduce the possibility of very recent expansions. For example, in the Great Lakes region, pronounced climatic change includes past glaciations as well as recent, rapid warming. Here we evaluate different expansion hypotheses with a genomic study of the white-footed mouse (Peromyscus leucopus noveboracensis), which is one of the most common mammals throughout the Great Lakes region. Ecological surveys coupled with historical museum records suggest a recent range expansion of P. leucopus associated with the warming climate over the last decades. These detailed records have yet to be complemented by genomic data that provide the requisite resolution for detecting recent expansion, although some mitochondrial DNA (mtDNA) sequences have suggested possible hypotheses about the geography of expansion. With more than 7,000 loci generated using RADseq, we evaluate support for multiple hypotheses of a geographic expansion in the Upper Peninsula of Michigan (UP). Analysis of a single random single-nucleotide polymorphism per locus revealed a fine-scale population structure separating the Lower Peninsula (LP) population from all other populations in the UP. We also detected a genetic structure that reflects an evolutionary history of postglacial colonization from two different origins into the UP, one coming from the LP and one coming from the west. Instead of supporting a climate-driven range expansion, as suggested by field surveys, our results support more ancient postglacial colonization of the UP from two different ancestral sources. With these results, we offer new insights about P. leucopus geographic expansion history, as well as a more general phylogeographic framework for testing range shifts in the Great Lakes region.
Tumor-Derived Cell Culture Model for the Investigation of Meningioma Biology
Authors: Uhlmann Erik J , Rabinovsky Rosalia , Varma Hemant , El Fatimy Rachid , Kasper Ekkehard M , Moore Justin M , Vega Rafael A , Thomas Ajith J , Alterman Ronald L , Stippler Martina , Anderson Matthew P , Uhlmann Erik N , Kipper Franciele C , Krichevsky Anna M 
Published: December 2021

Abstract
Meningioma is the most common primary central nervous system tumor. Although mostly nonmalignant, meningioma can cause serious complications by mass effect and vasogenic edema. While surgery and radiation improve outcomes, not all cases can be treated due to eloquent location. Presently no medical treatment is available to slow meningioma growth owing to incomplete understanding of the underlying pathology, which in turn is due to the lack of high-fidelity tissue culture and animal models. We propose a simple and rapid method for the establishment of meningioma tumor-derived primary cultures. These cells can be maintained in culture for a limited time in serum-free media as spheres and form adherent cultures in the presence of 4% fetal calf serum. Many of the tissue samples show expression of the lineage marker PDG2S, which is typically retained in matched cultured cells, suggesting the presence of cells of arachnoid origin. Furthermore, nonarachnoid cells including vascular endothelial cells are also present in the cultures in addition to arachnoid cells, potentially providing a more accurate tumor cell microenvironment, and thus making the model more relevant for meningioma research and high-throughput drug screening.
Creating and Disrupting Othering During Policymaking in a Polarized Context
Authors: Schraedley Megan K , Dougherty Debbie S 
Published: December 2021

Abstract
As the United States has become increasingly polarized, policymakers have had difficulty gaining bipartisan support for policy proposals. Political polarization can lead to the othering of individuals, a process characterized by the tendency to construct members of an opposing party in negative ways. In this article, we examine the creation and disruption of othering through the lens of language convergence/meaning divergence (LC/MD) and pragmatic ambiguity. LC/MD and pragmatic ambiguity framed our case study of the successful bipartisan passage of the Global Food Security Act (GFSA) in 2016. We found that othering was produced through a maestro Discourse of Polarization that structured interactions between other Discourses, including the Discourse of National Security and the Global Good Discourse. Discordant framings of the three Discourses created the ambiguity necessary to disrupt othering and achieve collective action. The findings provide new theoretical insights into othering processes while pragmatic ambiguity broadens LC/MD in important ways.
Systems-level analysis of the plasticity of the maize metabolic network reveals novel hypotheses in the nitrogen-use efficiency of maize roots
Authors: Seaver Samuel M D 
Published: December 2021

This article comments on:Chowdhury NB, Schroeder WL, Sarkar D, Amiour N, Quilleré I, Hirel B, Maranas CD, Saha R. 2022. Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions. Journal of Experimental Botany 73, 275–291.
Hen 3-860: new southern eclipsing symbiotic star observed in the outburst
Authors: Merc J , Gális R , Wolf M , Velez P , Bohlsen T , Barlow B N 
Published: December 2021

ABSTRACT
Brightening of Hen 3-860, previously classified as an Hα emitter, was detected by the All-Sky Automated Survey for Supernovae (ASAS-SN) survey at the end of the year 2016. We have obtained the first spectroscopic observations of the transient and supplemented them with photometric data from the Digital Access to a Sky Century at Harvard (DASCH) archive of astronomical plates, All-Sky Automated Survey (ASAS), and ASAS-SN surveys. Based on the results of our analysis, we can classify the object as a classical symbiotic star of the infrared type S, consisting of an M2-3 giant with a temperature of Tg ∼ 3550 K, a radius of Rg ∼ 60–75 R⊙, and a luminosity of Lg ∼ 540–760 L⊙, and a hot and luminous component (Th ∼ 1 × 105–2 × 105 K and $L_{\rm h}\, \sim 10^3\, L_\odot$). The system experienced at least four outbursts in the last 120 years. In addition to the outbursts, its light curves revealed the presence of eclipses of the hot component and its surrounding (relatively cool) shell, which developed during the outburst and redistributed a fraction of the radiation of the hot component into the optical, by the giant, classifying the object as a representative of a group of eclipsing symbiotic stars. The eclipses allowed us to reveal the orbital period of the system to be 602 d.
Constraining protoplanetary disc mass using the GI wiggle
Authors: Terry J P , Hall C , Longarini C , Lodato G , Toci C , Veronesi B , Paneque-Carreño T , Pinte C 
Published: December 2021

ABSTRACT
Exoplanets form in protoplanetary accretion discs. The total protoplanetary disc mass is the most fundamental parameter, since it sets the mass budget for planet formation. Although observations with the Atacama Large Millimeter/Submillimeter array (ALMA) have dramatically increased our understanding of these discs, total protoplanetary disc mass remains difficult to measure. If a disc is sufficiently massive (≳10 per cent of the host star mass), it can excite gravitational instability (GI). Recently, it has been revealed that GI leaves kinematic imprints of its presence known as the ‘GI Wiggle’. In this work, we use numerical simulations to determine an approximately linear relationship between the amplitude of the wiggle and the host disc-to-star mass ratio, and show that measurements of the amplitude are possible with the spatial and spectral capabilities of ALMA. These measurements can therefore be used to constrain disc-to-star mass ratio.
Impact of denosumab discontinuation on changes in bone mineral density and bone erosion in rheumatoid arthritis patients
Authors: Tanaka Sakae , Kobayashi Makiko , Saito Kengo , Takita Atsushi 
Published: December 2021

ABSTRACT

Objectives
This study investigated changes in bone mineral density (BMD) and erosion after denosumab discontinuation in rheumatoid arthritis (RA) patients without osteoporosis who participated in the DESIRABLE study.

Methods
This multicentre observational study consisted of a prediscontinuation visit (date of final assessment in DESIRABLE) and a postdiscontinuation visit (2.5 years after the last administered dose of denosumab). Percentage change in lumbar spine (LS) BMD from baseline was assessed as the primary endpoint.

Results
Fifty-nine patients were enrolled. The percentage change in LS BMD decreased to baseline levels at the postdiscontinuation visit. Compared with baseline, C-telopeptide of type I collagen levels increased after denosumab discontinuation but most patients had levels within the reference range. Bone erosion scores were not significantly different between the on-treatment period and after denosumab discontinuation (p = .0666) but there was a numerical increase postdiscontinuation. The progression in bone erosion score was significantly reduced in patients whose disease activity was in remission versus those not in remission (p = .0195).

Conclusions
In RA patients without osteoporosis, denosumab discontinuation can be explored while considering patient background factors (disease activity and risk of fracture) and accounting for progression of bone erosion and LS BMD decrease after withdrawal.
Identifying essential genes across eukaryotes by machine learning
Authors: Beder Thomas , Aromolaran Olufemi , Dönitz Jürgen , Tapanelli Sofia , Adedeji Eunice O , Adebiyi Ezekiel , Bucher Gregor , Koenig Rainer 
Published: December 2021

AbstractIdentifying essential genes on a genome scale is resource intensive and has been performed for only a few eukaryotes. For less studied organisms essentiality might be predicted by gene homology. However, this approach cannot be applied to non-conserved genes. Additionally, divergent essentiality information is obtained from studying single cells or whole, multi-cellular organisms, and particularly when derived from human cell line screens and human population studies. We employed machine learning across six model eukaryotes and 60 381 genes, using 41 635 features derived from the sequence, gene function information and network topology. Within a leave-one-organism-out cross-validation, the classifiers showed high generalizability with an average accuracy close to 80% in the left-out species. As a case study, we applied the method to Tribolium castaneum and Bombyx mori and validated predictions experimentally yielding similar performances. Finally, using the classifier based on the studied model organisms enabled linking the essentiality information of human cell line screens and population studies.
Advances in the management of breast cancer brain metastases
Authors: Sammons Sarah , Van Swearingen Amanda E D , Chung Caroline , Anders Carey K 
Published: December 2021

AbstractThe development of breast cancer (BC) brain metastases (BrM) is a common complication of advanced disease, occurring in up to half of the patients with advanced disease depending on the subtype. The management of BCBrM requires complex multidisciplinary care including local therapy, surgical resection and/or radiotherapy, palliative care, and carefully selected systemic therapies. Significant progress has been made in the human epidermal growth factor receptor 2-positive (HER2+) BCBrM population due to novel brain penetrable systemic therapies. Increased inclusion of patients with BCBrM in clinical trials using brain-penetrant systemic therapies recently led to the first FDA approval of a HER2-directed therapy specifically in the BCBrM population in the last year. Advances for the treatment of HR+/HER2− and TNBC BCBrM subgroups continue to evolve. In this review, we will discuss the diagnosis and multidisciplinary care of BCBrM. We focus on recent advances in neurosurgery, radiation therapy, and systemic treatment therapies with intracranial activity. We also provide an overview of the current clinical trial landscape for patients with BCBrM.
Surgical advances in the management of brain metastases
Authors: Ng Patrick R , Choi Bryan D , Aghi Manish K , Nahed Brian V 
Published: December 2021

Abstract
As the epidemiological and clinical burden of brain metastases continues to grow, advances in neurosurgical care are imperative. From standard magnetic resonance imaging (MRI) sequences to functional neuroimaging, preoperative workups for metastatic disease allow high-resolution detection of lesions and at-risk structures, facilitating safe and effective surgical planning. Minimally invasive neurosurgical approaches, including keyhole craniotomies and tubular retractors, optimize the preservation of normal parenchyma without compromising extent of resection. Supramarginal surgery has pushed the boundaries of achieving complete removal of metastases without recurrence, especially in eloquent regions when paired with intraoperative neuromonitoring. Brachytherapy has highlighted the potential of locally delivering therapeutic agents to the resection cavity with high rates of local control. Neuronavigation has become a cornerstone of operative workflow, while intraoperative ultrasound (iUS) and intraoperative brain mapping generate real-time renderings of the brain unaffected by brain shift. Endoscopes, exoscopes, and fluorescent-guided surgery enable increasingly high-definition visualizations of metastatic lesions that were previously difficult to achieve. Pushed forward by these multidisciplinary innovations, neurosurgery has never been a safer, more effective treatment for patients with brain metastases.
Dyskeratosis congenita: rare case report of Syria
Authors: Hussein Firas , Omar Zainab 
Published: December 2021

ABSTRACT
Dyskeratosis congenita (DC) is an inherited disease characterized by the triad of abnormal skin pigmentation, nail dystrophy and mucosal leukoplakia. Non-cutaneous abnormalities (dental, gastrointestinal, genitourinary, neurological, ophthalmic, pulmonary and skeletal) have also been reported. Bone marrow failure (BMF) is the main cause of early mortality, with an additional predisposition to malignancy. DC results from an anomalous progressive shortening of telomeres resulting in DNA replication problems inducing replicative senescence. Men are more affected than women are and X-linked recessive, autosomal dominant and autosomal recessive forms of the disease are recognized. There are no targeted therapies for DC. Patients treated with androgens had a hematological response. We herein describe case of a 32-year-old man, presented with several characteristic systemic features of this condition, including the classic triad of lesions, dysplastic bone marrow, epiphora and liver cirrhosis with grade I esophageal varices. Therefore, a prophylactic propranolol was started in additional to danazol. Three-week later, the patient had subsequent increases in his platelet, red cell and white cell counts.
Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription
Authors: Feng Yilong , Tao Shentong , Zhang Pengyue , Sperti Francesco Rota , Liu Guanqing , Cheng Xuejiao , Zhang Tao , Yu Hengxiu , Wang Xiu-e , Chen Caiyan , Monchaud David , Zhang Wenli 
Published: December 2021

AbstractA DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
Boron uptake in rice is regulated post-translationally via a clathrin-independent pathway
Authors: Huang Sheng , Konishi Noriyuki , Yamaji Naoki , Shao Ji Feng , Mitani-Ueno Namiki , Ma Jian Feng 
Published: December 2021

Abstract
Uptake of boron (B) in rice (Oryza sativa) is mediated by the Low silicon rice 1 (OsLsi1) channel, belonging to the NOD26-like intrinsic protein III subgroup, and the efflux transporter B transporter 1 (OsBOR1). However, it is unknown how these transporters cooperate for B uptake and how they are regulated in response to B fluctuations. Here, we examined the response of these two transporters to environmental B changes at the transcriptional and posttranslational level. OsBOR1 showed polar localization at the proximal side of both the exodermis and endodermis of mature root region, forming an efficient uptake system with OsLsi1 polarly localized at the distal side of the same cell layers. Expression of OsBOR1 and OsLsi1 was unaffected by B deficiency and excess. However, although OsLsi1 protein did not respond to high B at the protein level, OsBOR1 was degraded in response to high B within hours, which was accompanied with a significant decrease of total B uptake. The high B-induced degradation of OsBOR1 was inhibited in the presence of MG-132, a proteasome inhibitor, without disturbance of the polar localization. In contrast, neither the high B-induced degradation of OsBOR1 nor its polarity was affected by induced expression of dominant-negative mutated dynamin-related protein 1A (OsDRP1AK47A) or knockout of the mu subunit (AP2M) of adaptor protein-2 complex, suggesting that clathrin-mediated endocytosis is not involved in OsBOR1 degradation and polar localization. These results indicate that, in contrast to Arabidopsis thaliana, rice has a distinct regulatory mechanism for B uptake through clathrin-independent degradation of OsBOR1 in response to high B.
Diagnosing Physician Error: A Machine Learning Approach to Low-Value Health Care
Authors: Mullainathan Sendhil , Obermeyer Ziad 
Published: December 2021

Abstract
We use machine learning as a tool to study decision making, focusing specifically on how physicians diagnose heart attack. An algorithmic model of a patient’s probability of heart attack allows us to identify cases where physicians' testing decisions deviate from predicted risk. We then use actual health outcomes to evaluate whether those deviations represent mistakes or physicians’ superior knowledge. This approach reveals two inefficiencies. Physicians overtest: predictably low-risk patients are tested, but do not benefit. At the same time, physicians undertest: predictably high-risk patients are left untested, and then go on to suffer adverse health events including death. A natural experiment using shift-to-shift testing variation confirms these findings. Simultaneous over- and undertesting cannot easily be explained by incentives alone, and instead point to systematic errors in judgment. We provide suggestive evidence on the psychology underlying these errors. First, physicians use too simple a model of risk. Second, they overweight factors that are salient or representative of heart attack, such as chest pain. We argue health care models must incorporate physician error, and illustrate how policies focused solely on incentive problems can produce large inefficiencies.