bluuebunny/crossref_metadata_2025_split huggingface dataset:
HN-PPISP: a hybrid network based on MLP-Mixer for protein–protein interaction site prediction
Authors: Kang Yan , Xu Yulong , Wang Xinchao , Pu Bin , Yang Xuekun , Rao Yulong , Chen Jianguo 
Published: November 2022

AbstractMotivationBiological experimental approaches to protein–protein interaction (PPI) site prediction are critical for understanding the mechanisms of biochemical processes but are time-consuming and laborious. With the development of Deep Learning (DL) techniques, the most popular Convolutional Neural Networks (CNN)-based methods have been proposed to address these problems. Although significant progress has been made, these methods still have limitations in encoding the characteristics of each amino acid in protein sequences. Current methods cannot efficiently explore the nature of Position Specific Scoring Matrix (PSSM), secondary structure and raw protein sequences by processing them all together. For PPI site prediction, how to effectively model the PPI context with attention to prediction remains an open problem. In addition, the long-distance dependencies of PPI features are important, which is very challenging for many CNN-based methods because the innate ability of CNN is difficult to outperform auto-regressive models like Transformers.ResultsTo effectively mine the properties of PPI features, a novel hybrid neural network named HN-PPISP is proposed, which integrates a Multi-layer Perceptron Mixer (MLP-Mixer) module for local feature extraction and a two-stage multi-branch module for global feature capture. The model merits Transformer, TextCNN and Bi-LSTM as a powerful alternative for PPI site prediction. On the one hand, this is the first application of an advanced Transformer (i.e. MLP-Mixer) with a hybrid network for sequence-based PPI prediction. On the other hand, unlike existing methods that treat global features altogether, the proposed two-stage multi-branch hybrid module firstly assigns different attention scores to the input features and then encodes the feature through different branch modules. In the first stage, different improved attention modules are hybridized to extract features from the raw protein sequences, secondary structure and PSSM, respectively. In the second stage, a multi-branch network is designed to aggregate information from both branches in parallel. The two branches encode the features and extract dependencies through several operations such as TextCNN, Bi-LSTM and different activation functions. Experimental results on real-world public datasets show that our model consistently achieves state-of-the-art performance over seven remarkable baselines.AvailabilityThe source code of HN-PPISP model is available at https://github.com/ylxu05/HN-PPISP.
Muscarinic and NMDA Receptors in the Substantia Nigra Play a Role in Reward-Related Learning
Authors: Galaj Ewa , Barrera Eddy D , Lynch Olivia L , Diodati Rachel , Thomas Ashley , Schneider Piper , Lenhard Hayley , Vashisht Apoorva , Ranaldi Robert 
Published: November 2022

Abstract

Background
Reward-related learning, where animals form associations between rewards and stimuli (i.e., conditioned stimuli [CS]) that predict or accompany those rewards, is an essential adaptive function for survival.

Methods
In this study, we investigated the mechanisms underlying the acquisition and performance of conditioned approach learning with a focus on the role of muscarinic acetylcholine (mACh) and NMDA glutamate receptors in the substantia nigra (SN), a brain region implicated in reward and motor processes.

Results
Using RNAscope in situ hybridization assays, we found that dopamine neurons of the SN express muscarinic (mACh5), NMDA2a, NMDA2b, and NMDA2d receptor mRNA but not mACh4. NMDA, but not mACh5, receptor mRNA was also found on SN GABA neurons. In a conditioned approach paradigm, rats were exposed to 3 or 7 conditioning sessions during which light/tone (CS) presentations were paired with delivery of food pellets, followed by a test session with CS-only presentations. Intra-SN microinjections of scopolamine (a mACh receptor antagonist) or AP-5 (a NMDA receptor antagonist) were made either prior to each conditioning session (to test their effects on acquisition) or prior to the CS-only test (to test their effects on expression of the learned response). Scopolamine and AP-5 produced dose-dependent significant reductions in the acquisition, but not performance, of conditioned approach.

Conclusions
These results suggest that SN mACh and NMDA receptors are key players in the acquisition, but not the expression, of reward-related learning. Importantly, these findings redefine the role of the SN, which has traditionally been known for its involvement in motor processes, and suggest that the SN possesses attributes consistent with a function as a hub of integration of primary reward and CS signals.
Modeling the accident prediction for at-grade highway-rail crossings
Authors: Yang Xue , Li Joshua Qiang , Zhang Aonan (Allen) , Zhan You (Jason) 
Published: November 2022

Abstract
Since accidents at highway-rail at-grade crossings (HRGCs) are often catastrophic, safety prediction and evaluation at such locations are of great importance. In this paper, at-grade crossing inventory data and historical accident data were obtained from the Federal Railroad Administration (FRA’s) Office of Safety online databases. The HRGC railroad and highway characteristics were selected as the influencing variables. Considering HRGC accidents are over-dispersed count data with excessive zeros, six count data models, including the Poisson model, negative binomial model (NB), zero-inflated Poisson model (ZIP), zero-inflated negative binomial model (ZINB), hurdle Poisson (HP) model, and hurdle negative binomial model (HNB) were investigated and developed for accident prediction. The ZINB model outperformed the other five models in terms of the goodness-of-fit, zero inflations, and statistical significance of factors. The most significant contributing factors in the ZINB model included the maximum timetabled speed of train, exposure-related variables such as total through trains, highway traffic volume, rural or urban area, and the type of control devices at HRGCs, followed by the minimum speed of train, highway paved or not, and the number of traffic lanes. This study could assist decision-makers with more robust safety evaluation at highway-rail at-grade crossings.
Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep
Authors: Guo Yingwei , Bai Fengting , Wang Jintao , Fu Shaoyin , Zhang Yu , Liu Xiaoyi , Zhang Zhuangbiao , Shao Junjie , Li Ran , Wang Fei , Zhang Lei , Zheng Huiling , Wang Xihong , Liu Yongbin , Jiang Yu 
Published: November 2022

Abstract
The efficiency of molecular breeding largely depends on inexpensive genotyping arrays. In this study, we aimed to develop an ovine high-resolution multiple-single-nucleotide polymorphism (SNP) capture array, based on genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology. All the markers were from 40K captured regions, including genes located within selective sweep regions, breed-specific regions, quantitative trait loci (QTL), and the potential functional SNPs on the sheep genome. The results showed that a total of 210K high-quality SNPs were identified in the 40K regions, indicating a high average capture ratio (99.7%) for the target genomic regions. Using genotyped data (n = 317) from liquid chip technology, we further performed genome-wide association studies (GWAS) to detect the genetic loci affecting sheep hair types and teat number. A single signiﬁcant association signal for hair types was identified on 6.7-7.1 Mb of chromosome 25. The IRF2BP2 gene (chr25: 7,067,974-7,071,785), which is located within this genomic region, has been previously known to be involved in hair/wool traits in sheep. The results further showed a new candidate region around 26.4 Mb of chromosome 13, between the ARHGAP21 and KIAA1217 genes, that was significantly related to teat number in sheep. The haplotype patterns of this region also showed differences in animals with 2, 3, or 4 teats. Advances in using the high-accuracy and low-cost liquid chip are expected to accelerate sheep genomic and breeding studies in the coming years.
Serum metabolomic characterization in pigs in relation to birth weight category and neonatal nutrition
Authors: Wellington Michael O , Rodrigues Lucas A , Quinn Melissa A , Panisson Josiane C , Ferguson David P , Columbus Daniel A 
Published: November 2022

AbstractThe objective of this study was to characterize developmental differences in low birth weight (LBW) and normal birth weight (NBW) piglets with or without pre-weaning nutrient restriction using serum metabolomic profile analysis. At farrowing, 112 piglets were identified as LBW (1.22 ± 0.28 kg) or NBW (1.70 ± 0.27 kg) and were randomly assigned to receive normal nutrition (NN) or restricted nutrition (RN) (6 h/day no suckling) from days 2 to 28 post farrow (n = 8 pigs/group). On day 28, piglets were weaned onto a common diet. Fasted blood samples were obtained on days 28 and 56 (n = 8 pigs/group) and were analyzed using quantitative metabolomics via a combination of direct injection mass spectrometry with a reverse-phase LC–MS/MS custom assay. Data were normalized using logarithmic transformation and auto-scaling. Partial least squares discriminant analysis (PLS-DA) was carried out to further explore the differential metabolites among the groups (metaboanalyst.ca) with an integrated enrichment and pathway topography analysis. On day 28, LBW piglets had lower levels of essential amino acids as well as reduced metabolites associated with fatty acid oxidation, glycolysis, and the tri-carboxylic acid (TCA) cycle compared to the NBW group. The overall reduction of metabolites associated with energy production and regulation suggests that LBW vs. NBW are in an energy-survival state. On day 56, LBW pigs had increased utilization of fatty acids and resultant ketone production, evident by increased carnitines, acetoacetate, β-hydroxybutyrate, and glycerol compared to NBW pigs. In addition, compared to the NBW pigs LBW pigs had a consistent decrease in serum glucose and lactate as well as reduced TCA cycle metabolites: pyruvate, succinate, citrate, and α-ketoglutaric acid similar to day 28. Low reliance on glycolysis and the TCA cycle and higher glycerol production in the LBW pigs may indicate impairments in glucose tolerance at 56 d. In summary, LBW piglets appear to have more metabolic alterations in early life, which is not resolved with adequate nutrition or refeeding and may elucidate physiological and metabolic mechanisms of poor growth and life performance compared to NBW pigs later in life.
Qi Wei Anti-burn Tincture Remodels Liver Metabolic Pathways and Treats Burn Wounds Efficiently
Authors: Wang Shuai , Zhou Hui , Cui Weiqi , Zhang Junwei , Wu Deqiao , Zhang Nan , Xu Xia 
Published: November 2022

Abstract
This work aims to elucidate the molecular mechanism of Qi Wei anti-burn Tincture (QW) on wound healing in burnt mice using metabolomics and molecular biology techniques. A scald model was first established in Kunming mice. After treatment, biochemical indicators for liver function and burnt skin tissues were then evaluated via biochemical detection and HE staining, respectively. Liver tissues were further analyzed for differential metabolites, inflammatory factors, and mRNA levels of cytokines using metabolomics and molecular biology techniques. Involved metabolic pathways were also identified using software. QW treatment did promote the healing of the burn wounds in Kunming mice with a downregulation of ALP, ALT, and AST to normal levels. In mouse liver tissue, the contents of glutamine, aspartic acid, and citrulline were significantly reduced, while the contents of 5-hydroxyproline, taurine, hypotaurine, and glutamic acid significantly increased. These major differential compounds are involved in the arginine metabolic pathway, nitrogen excretion, and the metabolism of taurine and hypotaurine, suggesting that QW reprogramed the above metabolic processes in the liver. Furthermore, the application of QW increased the expression of TGF-β1 and FGF-2 and reduced the levels of TNF-α, IL-1β, IL-6, and reactive oxygen species in the liver of mice induced by burn injury. This study found that QW treatment promoted metabolic pathway remodeling in the liver, which might be a potential mechanism for QW to treat burn wounds.
Two Cases of COVID-19 Patients With Associated Purpura Fulminans
Authors: Pangburn Jane , Gibbs Jeffrey 
Published: November 2022

AbstractPurpura fulminans (PF) is a life-threatening emergency involving coagulopathy and widespread skin necrosis. Early treatment, especially surgical management, is imperative as prognosis can be very poor. PF is most commonly associated with severe bacterial illness; however, viral causes are also possible. Currently in the literature, there have only been a handful of PF cases associated with COVID-19. We present two cases of PF in the setting of COVID-19 infection. Both patients had a history of underlying coagulopathies. PF can be a sign of underlying coagulopathy in a COVID-19 patient, who is already at increased risk for thromboembolic events due to the inflammatory nature of COVID itself. Due to how quickly PF can develop into life-threatening necrosis and multiorgan failure, it is imperative that these patients are referred early to a burn center for more advanced care.
Comparison of dosimetries of carbon-ion pencil beam scanning, proton pencil beam scanning and volumetric modulated arc therapy for locally recurrent rectal cancer
Authors: Mori Shinichiro , Bhattacharyya Tapesh , Furuichi Wataru , Tohyama Naoki , Nomoto Akihiro , Shinoto Makoto , Takiyama Hirotoshi , Yamada Shigeru 
Published: November 2022

Abstract
We compared the dose distributions of carbon-ion pencil beam scanning (C-PBS), proton pencil beam scanning (P-PBS) and Volumetric Modulated Arc Therapy (VMAT) for locally recurrent rectal cancer.
The C-PBS treatment planning computed tomography (CT) data sets of 10 locally recurrent rectal cancer cases were randomly selected. Three treatment plans were created using identical prescribed doses. The beam angles for C-PBS and P-PBS were identical. Dosimetry, including the dose received by 95% of the planning target volume (PTV) (D95%), dose to the 2 cc receiving the maximum dose (D2cc), organ at risk (OAR) volume receiving &gt; 15Gy (V15) and &gt; 30Gy (V30), was evaluated. Statistical significance was assessed using the Wilcoxon signed-rank test. Mean PTV-D95% values were &gt; 95% of the volume for P-PBS and C-PBS, whereas that for VMAT was 94.3%. However, PTV-D95% values in P-PBS and VMAT were &lt; 95% in five and two cases, respectively, due to the OAR dose reduction. V30 and V15 to the rectum/intestine for C-PBS (V30 = 4.2 ± 3.2 cc, V15 = 13.8 ± 10.6 cc) and P-PBS (V30 = 7.3 ± 5.6 cc, V15 = 21.3 ± 13.5 cc) were significantly lower than those for VMAT (V30 = 17.1 ± 10.6 cc, V15 = 55.2 ± 28.6 cc). Bladder-V30 values with P-PBS/C-PBS (3.9 ± 4.8 Gy(RBE)/3.0 ± 4.0 Gy(RBE)) were significantly lower than those with VMAT (7.9 ± 8.1 Gy). C-PBS provided superior dose conformation and lower OAR doses compared with P-PBS and VMAT. C-PBS may be the best choice for cases in which VMAT and P-PBS cannot satisfy dose constraints. C-PBS could be another choice for cases in which VMAT and P-PBS cannot satisfy dose constraints, thereby avoiding surgical resection.
Sarcomatoid mesothelioma: unusual findings and literature review
Authors: Clopton Brittni , Long Winnie , Santos Monica , Asarian Armand , Genato Romulo , Xiao Philip 
Published: November 2022

AbstractSarcomatoid mesothelioma is an aggressive disease secondary to its propensity to undergo rapid growth, show inconsistent expression of tumor markers and invade surrounding tissues. Therefore, there are numerous obstacles that clinical researchers face as they look for new methods to diagnose and treat the malignancy. We present a case of sarcomatoid mesothelioma, originally thought to be metastasis from renal cell carcinoma.
Combined pantaloon and femoral hernia: a common pathology in medicine occurring simultaneously
Authors: Rajkumar Karnan , Trivedi Aakash , Molavi Ida , Talishinskiy Toghrul 
Published: November 2022

Abstract
Inguinal hernias are typically classified based on their location and can be divided into two types. The most commonly seen inguinal hernias are direct and indirect, which can both potentially require surgical intervention. When both types of hernias are seen simultaneously, it is classified as a pantaloon hernia. This case describes an instance of a femoral hernia being found along with a pantaloon hernia. We present a case of what was projected to be a common inguinal hernia repair but progressed to a rare presentation of a femoral hernia superimposed on a pantaloon hernia. Pantaloon hernias plus a femoral hernia is a rare defect that does not present as often as the different types of isolated hernias.
Late presentation of midgut malrotation in a young adult
Authors: Lodhia Jay , Salewi Anande Kumbwaeli , Sway Happiness , Sadiq Adnan , Msuya David 
Published: November 2022

Abstract
Midgut malrotation is a congenital anomaly due to partial or complete failure of rotation of the midgut in fetal life. Majority of the cases present in the neonatal period and 90% within the first year. Adult presentation is rare and the true incidence is unknown as some cases pass undiagnosed. Whirlpool sign is pathognomic for midgut malrotation and management involves surgery.
Unroofing osteotomy for dissociated tibial intramedullary magnetic rod during implant removal: a case report
Authors: Dharamsi Miraal , Castagno Christopher , Klahs Kyle J , Abdelgawad Amr , Thabet Ahmed M 
Published: November 2022

Abstract
The PRECICE® intramedullary rod (NuVasive, San Diego, CA) utilizes multiple telescopic components to magnetically drive limb lengthening. These devices are routinely explanted after desired growth correction is met. To the author’s knowledge, this is the first description of an osteotomy assisted extraction of a disassociated tibial magnetic lengthening rod. A 17-year-old girl with fibular hemimelia and resolved left tibial length discrepancy after successful surgical lengthening underwent a complex implant removal approximately seven years after regenerate consolidation. During implant removal, the telescopic portion of the rod remained lodged in the tibial medullary canal and a subsequent unroofing osteotomy of the tibia was performed. Tibial limb length discrepancies are oftentimes corrected with complex implants comprised of multiple fragile components that are routinely explanted. During the unfortunate event of a telescopic intramedullary rod dissociation, an unroofing osteotomy can be successfully performed to removal all implant components.
Fibrous dysplasia of the sphenoid sinus: headache relieved by surgical excision—a case report
Authors: Jawad Jamal , Al-Domaidat Derar , Abaza Mohamed 
Published: November 2022

Abstract
Fibrous dysplasia (FD) is an uncommon benign bone disorder of unknown etiology in which normal medullary bone is replaced by fibrotic and osseous tissue. FD of paranasal sinuses is usually secondary to extension from adjacent bones. It is rarely limited to the sinuses, let alone limited to the sphenoid sinus. Furthermore, the relationship between headache and FD of paranasal sinuses has not been well addressed. We report a case of a 55-year-old female with FD of sphenoid sinuses complaining of sever right-sided parietal headache. Her headache was significantly improved after surgical excision of FD.
A case of anterior choroidal artery injury after resection of a pilocytic astrocytoma in the amygdale—a case report
Authors: Moustafa Wahab , Karamani Lydia , Schreiber Stefan 
Published: November 2022

Abstract
The anterior choroidal artery (AChA) arises from the last segment of internal carotid artery (ACI), the communicating C7 segment and comprises the terminal branch of ACI. Anatomical its origin located supraclionoidal after the ophthalmic C6 segment of ACI and after the rise of posterior communicating artery. The AChA gains greater importance because of its small size and its region of blood supply. With its perforating branches supplies important intracranial structures such as the optic tract, the posterior limb of the internal capsule, the lateral geniculate body, the medial temporal lobe and the medial area of the pallidum. The anterior choroidal artery is a fine artery and consists of two parts, a cisternal and a plexal one. There are only few studies published, which describe the exact anatomy and the impact of its damage. On the present report, we discuss a case of an iatrogenic injury of the anterior choroidal artery and its hazardous consequences.
Cholecystocolonic fistula: two different presentations of this rare complication of gallstones
Authors: Salas-Parra Ruben D , Hattingh Genevieve , Shumway Karlie R , Esposito Kathryn , Lois William , Farkas Daniel T 
Published: November 2022

Abstract
Cholecystocolonic fistulas (CCF) are a rare but significant complication of biliary disease, frequently presenting as gallstone ileus. Although there is no one agreed-upon procedure, enterolithotomy appears to be the initial treatment of choice; with a subsequent cholecystectomy performed ~4–8 weeks later. Alternatively, a patient may undergo a single-stage procedure, at which time an enterolithotomy, cholecystectomy and fistula closure are performed. Herein, we describe two patients with chronic cholecystitis and subsequent development of CCF with differing presentations. We report the clinical, radiographic and intraoperative findings and discuss the surgical treatment options for each patient, respectively.
A successful management of left-sided posterior congenital diaphragmatic hernia of the jejunum, ileum, colon and left kidney: a case report
Authors: Al-Abdullah Zainab , Duvuru Ruthwik , Nawaz Faisal A , Ennab Farah , Alklani Temaa , Ahmed Aftab 
Published: November 2022

Abstract
Congenital diaphragmatic hernia (CDH) is a rare developmental anomaly in which abdominal contents herniate into the thoracic cavity due to underdevelopment of the diaphragm, possibly leading to pulmonary hypoplasia. Whereas surgery is not the first priority in treatment, it must be performed within a window of 2 weeks and after hemodynamic stability has been achieved. The patient described in this case report had a CDH of the jejunum, ileum, colon and left kidney diagnosed in a boy of South Asian origin who presented with tachypnea in the third hour of life. Imaging studies conducted included chest X-ray, chest ultrasound including echocardiogram, and abdominal and pelvic ultrasound. Treatment and management were successful despite complications. Future research on CDH is warranted in the populations in the Middle East, and local guidelines must be generated in order to improve diagnosis, treatment and prognosis.