bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forecasting the future clinical events of a patient through contrastive learning
Authors: Zhang Ziqi , Yan Chao , Zhang Xinmeng , Nyemba Steve L , Malin Bradley A 
Published: June 2022

Abstract

Objective
Deep learning models for clinical event forecasting (CEF) based on a patient’s medical history have improved significantly over the past decade. However, their transition into practice has been limited, particularly for diseases with very low prevalence. In this paper, we introduce CEF-CL, a novel method based on contrastive learning to forecast in the face of a limited number of positive training instances.

Materials and Methods
CEF-CL consists of two primary components: (1) unsupervised contrastive learning for patient representation and (2) supervised transfer learning over the derived representation. We evaluate the new method along with state-of-the-art model architectures trained in a supervised manner with electronic health records data from Vanderbilt University Medical Center and the All of Us Research Program, covering 48 000 and 16 000 patients, respectively. We assess forecasting for over 100 diagnosis codes with respect to their area under the receiver operator characteristic curve (AUROC) and area under the precision-recall curve (AUPRC). We investigate the correlation between forecasting performance improvement and code prevalence via a Wald Test.

Results
CEF-CL achieved an average AUROC and AUPRC performance improvement over the state-of-the-art of 8.0%–9.3% and 11.7%–32.0%, respectively. The improvement in AUROC was negatively correlated with the number of positive training instances (P &lt; .001).

Conclusion
This investigation indicates that clinical event forecasting can be improved significantly through contrastive representation learning, especially when the number of positive training instances is small.
In vivo investigation of ruminant placenta function and physiology—a review
Authors: Tanner Amelia R , Kennedy Victoria C , Lynch Cameron S , Hord Taylor K , Winger Quinton A , Rozance Paul J , Anthony Russell V 
Published: June 2022

Abstract
The placenta facilitates the transport of nutrients to the fetus, removal of waste products from the fetus, immune protection of the fetus and functions as an endocrine organ, thereby determining the environment for fetal growth and development. Additionally, the placenta is a highly metabolic organ in itself, utilizing a majority of the oxygen and glucose derived from maternal circulation. Consequently, optimal placental function is required for the offspring to reach its genetic potential in utero. Among ruminants, pregnant sheep have been used extensively for investigating pregnancy physiology, in part due to the ability to place indwelling catheters within both maternal and fetal vessels, allowing for steady-state investigation of blood flow, nutrient uptakes and utilization, and hormone secretion, under non-stressed and non-anesthetized conditions. This methodology has been applied to both normal and compromised pregnancies. As such, our understanding of the in vivo physiology of pregnancy in sheep is unrivalled by any other species. However, until recently, a significant deficit existed in determining the specific function or significance of individual genes expressed by the placenta in ruminants. To that end, we developed and have been using in vivo RNA interference (RNAi) within the sheep placenta to examine the function and relative importance of genes involved in conceptus development (PRR15 and LIN28), placental nutrient transport (SLC2A1 and SLC2A3), and placenta-derived hormones (CSH). A lentiviral vector is used to generate virus that is stably integrated into the infected cell’s genome, thereby expressing a short-hairpin RNA (shRNA), that when processed within the cell, combines with the RNA Induced Silencing Complex (RISC) resulting in specific mRNA degradation or translational blockage. To accomplish in vivo RNAi, day 9 hatched and fully expanded blastocysts are infected with the lentivirus for 4 to 5 h, and then surgically transferred to synchronized recipient uteri. Only the trophectoderm cells are infected by the replication deficient virus, leaving the inner cell mass unaltered, and we often obtain ~70% pregnancy rates following transfer of a single blastocyst. In vivo RNAi coupled with steady-state study of blood flow and nutrient uptake, transfer and utilization can now provide new insight into the physiological consequences of modifying the translation of specific genes expressed within the ruminant placenta.
Naturally occurring androgen excess cows are present in dairy and beef herds and have similar characteristics to women with PCOS
Authors: Abedal-Majed Mohamed A , Springman Shelby A , Jafar Hanan D , Bell Brooke E , Kurz Scott G , Wilson Kyle E , Cupp Andrea S 
Published: June 2022

Abstract
Beef cows with excess androstenedione (A4; High A4) in follicular fluid (FF) and secreted by the ovarian cortex have been reported from the University of Nebraska–Lincoln physiology herd displaying characteristics reminiscent of polycystic ovary syndrome (PCOS). Thus, we hypothesized that naturally occurring High A4 cows were present in other dairy and beef herds. Fourteen Jordan (Amman, Jordon) dairy heifers and 16 U.S. Meat Animal Research Center beef heifers were classified by FF (High A4: A4 &gt; 40 ng/mL and Control: A4 &lt; 20 ng/mL) and/or cortex culture media (High A4 &gt; 1 ng/mL/d or Control &lt; 1 ng/mL/d). High A4 dairy heifers (n = 6) had greater A4 concentrations (7.6-fold) in FF and (98-fold) greater in ovarian cortex culture media with greater numbers of primordial and fewer later-stage follicles than Controls (n = 8) even after 7 d of culture. Also, the ovarian cortex had greater staining for Picro Sirius red in High A4 dairy heifers compared with Controls indicating increased fibrosis. Thecal cells from High A4 dairy heifers had greater STAR, LHCGR, CYP17A, CD68, and PECAM mRNA expression with increased mRNA abundance of CYP17A1 and CD68 in the ovarian cortex cultures compared with Control dairy heifers. Similarly, cortex culture media from High A4 beef heifers (n = 10) had increased A4 (290-fold; P ≤ 0.001), testosterone (1,427-fold; P ≤ 0.001), and progesterone (9-fold; P ≤ 0.01) compared with Control heifers with increased primordial follicles and decreased later-stage follicles even after 7 d of culture, indicating abnormal follicular development. High A4 ovarian cortex cultures from beef heifers also had increased fibrosis markers and greater expression of PECAM (P = 0.01) with a tendency for increased vascular endothelial cadherin compared with Controls (n = 6). These two trials support our hypothesis that naturally occurring androgen excess cows are present in other dairy and beef herds. The ability to identify these females that have excess A4 ovarian microenvironments may allow for their use in understanding factors causing abnormal follicle development linked to androgen excess and inflammation.
Maternal nutrient restriction and over-feeding during gestation alter expression of key factors involved in placental development and vascularization
Authors: Reed Sarah A , Ashley Ryan , Silver Gail , Splaine Caitlyn , Jones Amanda K , Pillai Sambhu M , Peterson Maria L , Zinn Steven A , Govoni Kristen E 
Published: June 2022

Abstract
Poor maternal nutrition can negatively affect fetal and placental growth and development. However, the mechanism(s) that contribute to altered placenta growth and function are not well understood. We hypothesized that poor maternal diet would impact signaling through the C-X-C motif chemokine ligand (CXCL) 12-CXCL4 axis and/or placental expression of the insulin-like growth factor (IGF) axis. Using our established sheep model of poor maternal nutrition, we examined the effects of restricted- and over-feeding on ewe placentome gene and protein expression. Specifically, ewes were fed a control (CON; 100%), restricted (RES; 60%), or over (OVER; 140%) diet beginning at day 30.2 ± 0.02 of gestation, and samples were collected at days 45, 90, and 135 of gestation, representing periods of active placentation, peak placental growth, and near term, respectively. Placentomes were separated into cotyledon and caruncle, and samples snap frozen. Protein was determined by western blot and mRNA expression by real-time PCR. Data were analyzed by ANOVA and significance determined at P ≤ 0.05. Ewes fed a RES diet had decreased CXCL12 and vascular endothelial growth factor (VEGF), and increased tumor necrosis factor (TNF)α protein compared with CON ewes in caruncle at day 45 (P ≤0.05). In day 45 cotyledon, CXCR7 protein was increased and mTOR was decreased in RES relative to CON (P ≤0.05). At day 90, CXCR4 and CXCR7 were reduced in RES caruncle compared with CON, whereas VEGF was reduced and mTOR increased in cotyledon of RES ewes relative to CON (P ≤0.05). In OVER caruncle, at day 45 CXCR4 and VEGF were reduced and at day 90 CXCR4, CXCR7, and TNFα were reduced in caruncle compared with CON (P ≤0.05). There was no observed effect of OVER diet on protein abundance in the cotyledon (P &gt; 0.05). Expression of IGF-II mRNA was increased in OVER at day 45 and IGFBP-3 was reduced in RES at day 90 in caruncle relative to CON (P ≤0.05). Maternal diet did not alter placentome diameter or weight (P &gt; 0.05). These findings suggest that restricted- and over-feeding negatively impact protein and mRNA expression of key chemokines and growth factors implicated in proper placenta development and function.
Constant light exposure in early life induces m6A-mediated inhibition of IGF gene family in the chicken
Authors: Yang Yang , Xu Peirong , Liu Jie , Zhao Mindie , Cong Wei , Han Wanwan , Wang Deyun , Zhao Ruqian 
Published: June 2022

AbstractInsulin-like growth factor (IGF) family plays important roles in regulating the development of various organ systems through stimulating cell proliferation and differentiation. Photoperiod is an important factor affecting growth and development in the chicken, yet the effect of constant light exposure in early life on IGF1 and IGF2 expression in the chicken remains unclear. In this study, one-day-old chickens were kept in either constant light (24L:0D, LL) or natural photoperiod (12L:12D, LD) for the first week of life and then maintained in constant light from 8 to 21 d of age. Constant light exposure in early life reduced mRNA expression of IGF gene family, including mRNA expression of IGF1, IGF2, and IGF2 binding proteins, in the hippocampus, hypothalamus, and liver of chickens at both 7 and 21 d of age. Moreover, constant light exposure increased mRNA expression of genes involved in RNA methylation N6-methyladenosine (m6A) in a tissue-specific manner. Interestingly, higher m6A on 3ʹUTR of IGF2 mRNA coincides with lower IGF2 mRNA, indicating a possible role of m6A in the post-transcriptional regulation of IGF2 expression in the hippocampus, hypothalamus, and liver of chickens. These findings suggest a m6A-mediated gene regulation of IGF gene family in different organs of chicken and expand our knowledge on mechanism of gene regulation in response to early life experience.
Dose-response relationship between dietary choline and serum lipid profile, energy expenditure, and respiratory quotient in overweight adult cats fed at maintenance energy requirements
Authors: Rankovic Alexandra , Godfrey Hannah , Grant Caitlin E , Shoveller Anna K , Bakovic Marica , Kirby Gordon , Verbrugghe Adronie 
Published: June 2022

AbstractCholine is an essential nutrient linked to hepatic lipid metabolism in many animal species, including cats. The current study investigated the serum lipid profiles, serum liver enzymes, respiratory quotients, and energy expenditures of overweight cats fed maintenance diets, in response to graded doses of supplemental dietary choline. Overweight (body condition score [BCS]: ≥6/9) adult male neutered cats (n = 14) were supplemented with five choline chloride doses for 3-wk periods, in a 5 × 5 Latin square design. Doses were based on individual body weight (BW) and the daily recommended allowance (RA) for choline (63 mg/kg BW0.67) according to the National Research Council. Doses were control (no additional choline: 1.2 × RA, 77 mg/kg BW0.67), 2 × RA (126 mg/kg BW0.67), 4 × RA (252 mg/kg BW0.67), 6 × RA (378 mg/kg BW0.67), and 8 × RA (504 mg/kg BW0.67). Choline was top-dressed over the commercial extruded cat food (3,620 mg choline/kg diet), fed once a day at maintenance energy requirements (130 kcal/kgBW0.4). Body weight and BCS were assessed weekly. Fasted blood samples were taken and indirect calorimetry was performed at the end of each 3-wk period. Serum was analyzed for cholesterol, high-density lipoprotein cholesterol (HDL-C), triglycerides, non-esterified fatty acids, glucose, creatinine, blood urea nitrogen (BUN), alkaline phosphatase (ALP), and alanine aminotransferase. Very low-density lipoprotein cholesterol (VLDL) and low-density lipoprotein cholesterol were calculated. Data were analyzed via SAS using proc GLIMMIX, with group and period as the random effects, and treatment as the fixed effect. Statistical significance was considered at P &lt; 0.05. Body weight and BCS did not change (P &gt; 0.05). Serum cholesterol, HDL-C, triglycerides, and VLDL increased with 6 × RA (P &lt; 0.05). Serum ALP decreased with 8 × RA (P = 0.004). Choline at 4 × and 6 × RA decreased serum BUN (P = 0.006). Fed or fasted respiratory quotient and energy expenditure did not differ among dietary choline doses (P &gt; 0.05). These results suggest that dietary choline supplementation at 6 × RA may increase hepatic fat mobilization through increased lipoprotein transport and beneficially support hepatic health in overweight cats. Future studies that combine these results with existing knowledge of feline weight loss and hepatic lipidosis are warranted.
Association of a home-based nursing service during chemotherapy with the transfer to home care immediately after the last chemotherapy treatment in patients with advanced cancer
Authors: Higashibata Takahiro , Iwata Naoko , Kazama Ikuko , Irie Yoshiko , Yokosuka Kyoko , Okita Junya , Hamano Jun , Nagaoka Hiroka 
Published: June 2022

Abstract

Background
The appropriate timing of introducing the home-based nursing service to patients with advanced cancer has not been clarified. This study conducted a retrospective cohort study to investigate the associations of the early utilization of the home-based nursing service during chemotherapy with the place of care immediately after the last chemotherapy treatment in patients with advanced cancer.

Methods
Among the patients referred to the palliative care team of the University of Tsukuba Hospital between January 2018 and December 2019, patients with advanced cancer undergoing chemotherapy or before the start of chemotherapy at referral were included. The study patients who utilized the home-based nursing service during chemotherapy were classified into the early utilization group. The primary endpoint was the place of care immediately after the last chemotherapy treatment.

Results
Of the 1154 patients referred to the palliative care team during the study period, 261 were eligible for this study. Of these patients, 15.3% of patients (n = 40) received the home-based nursing service during chemotherapy. The proportion of patients transferred to home care after the last chemotherapy treatment was 17.5% in the early utilization group and 7.2% in the control group. The multivariate analysis revealed that the early utilization of the home-based nursing service during chemotherapy was significantly associated with the transfer to home care (odds ratio = 3.077; 95% confidence interval, 1.113–8.502).

Conclusion
The early utilization of the home-based nursing service during chemotherapy might be associated with the transfer to home care immediately after the last chemotherapy treatment.
Development and Intrapuparial Characterization of Hydrotaea aenescens (Diptera: Muscidae) Raised at Different Temperatures Under Laboratory Conditions
Authors: Duarte Marina Lopes , Queiroz Margareth Maria de Carvalho 
Published: June 2022

Abstract
Species belonging to the Muscidae family are important in the medical-sanitary and forensic fields due to their biology. The intrapuparial stage of Hydrotaea aenescens (Wiedemann, 1830), which represents about 50% of the immature development cycle in muscoid Diptera, has not yet been studied in detail. This study identifies and describes the main temporal morphological changes that occur in the pupal body of H. aenescens during its development at 22, 27, and 32 ± 1°C, RH 60 ± 10% with a 12-hr photoperiod. Ten pupae were collected, sacrificed, and fixed every 3 hr after pupariation up to 24 hr, and every 6 hr thereafter until the first emergence. Emergence took place at 282, 174, and 126 hr at 22, 27, and 32°C, with 520, 340, and 260 pupae, respectively. External morphology was described and recorded at eight development stages: pupariation, pre-pupae, early and late cryptocephalic pupae, phanerocephalic pupae, pupae-adult apolysis, pharate adults, and imago, employing 18 key morphological characters for pupae age. These morphological pupae characters, comprise, therefore an alternative and/or additional method to aid in determining the minimum Postmortem Interval (minPMI).
Lumbar discal cyst and post-operative discal pseudocyst: a case series
Authors: Jadhav Neha , Sivakumar Lawrence , Talibi Sayed Samed , Momoh Pearl , Rasul Fahid , Hussain Rahim , Shad Amjad 
Published: June 2022

Abstract
Four cases of lumbar cyst (2 discal cysts and 2 post-operative discal pseudocysts) who presented predominantly with features of sciatica without any motor, sensory or sphincteric disturbances. The patients were treated conservatively, and the management was aimed to avert any untoward surgical intervention taking into consideration patient safety and care. Two had previous lumbar decompressive discectomy. During the mean follow-up period of 13 months, there was progressive recovery of symptoms in all our 4 patients. All our patients were successfully managed by conservative approach. An intervertebral disc cyst should be considered in young patients in the differential diagnosis of any extradural intraspinal mass ventral to the thecal sac, notwithstanding its rarity. Alongside, conservative management can be offered as first line of management with appropriate patient selection that is absence of any motor/sensory/sphincteric disturbances. Facetal micro-instability could be one of the aetiologies of this pathology which necessitates further study.
Killing the Letter: Alternate Literacies and Orthographic Distortions in Jude the Obscure
Authors: Creechan Louise 
Published: June 2022

Abstract
When Jude the Obscure (1895) was published as a single volume novel, Hardy added the biblical epithet ‘the letter killeth’ to the title page. In Jude and across his works, Hardy revels in moments in which literacy seems to undo itself. This article traces Hardy’s attempts to ‘kill the letter’ through non-standard engagements with orthography as part of a larger proto-modernist approach that destabilizes the fixity of meaning. There are several concerns linked to the growing primacy of literacy that appear time and again in Hardy’s novels, specifically: the alternative literacies of the lesser educated, semiotic multiplicities, and the transformative potential of spelling mistakes. I suggest that Hardy’s treatment of these themes demonstrates a sustained effort to ‘kill the letter’ and challenge the assumption of progress made by the various educational reforms that had taken place in the latter half of the nineteenth century.
Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference
Authors: Smith Megan L. , Vanderpool Dan , Hahn Matthew W. 
Published: June 2022

Abstract
Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.