bluuebunny/crossref_metadata_2025_split huggingface dataset:
WATCHMEN: a case report highlighting the closure of a bilobed left atrial appendage using two WATCHMAN-FLX devices
Authors: Sood Abhinav , Kalavakunta Jagadeesh K , Gourineni Venu , Gupta Vishal 
Published: December 2023

Abstract

Background
Left atrial appendage occlusion (LAAO) performed percutaneously has emerged as a widely accepted method for stroke prevention, offering a viable alternative to anticoagulation. Numerous studies have demonstrated the effectiveness and safety of this procedure. However, in certain cases, the use of a single LAAO device may not adequately achieve optimal closure due to variations in the anatomy of the left atrial appendage (LAA).

Case summary
In this manuscript, we highlight the successful closure of a bilobed LAA with a large ostium utilizing two WATCHMAN™ FLX devices and using the double sheath technique. The aim was to achieve optimal closure and address the unique anatomical characteristics of the patient’s LAA.

Discussion
The utilization of two LAAO devices in bilobed appendage anatomy, where a single device may not be sufficient, is possible, although it poses a challenge because of the lack of technical expertise and limited published evidence. Transoesophageal imaging can serve as a valuable tool for assessing the precise anatomy of the LAA and guide the selection and placement of the occlusion devices.
Altered Bile Acid and Pouch Microbiota Composition in Patients With Chronic Pouchitis
Authors: Santiago Priscila , Quinn Kevin P , Chen Jun , Friton Jessica J , Rypstra Chad R , Kashyap Purna C , Raffals Laura E 
Published: December 2023

Abstract

Background
Patients with ulcerative colitis and total abdominal proctocolectomy with ileal pouch-anal anastomosis have a 50% risk of pouchitis and a 5% to 10% risk of chronic pouchitis.

Aims
The goal of the study was to compare pouch microbiota and stool bile acid composition in patients with chronic pouchitis, chronic pouchitis and primary sclerosing cholangitis, and normal pouch.

Methods
Patients with ulcerative colitis and ileal pouch-anal anastomosis were recruited from March 20, 2014, to August 6, 2019, and categorized into normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis groups. Stool samples were subjected to bile acid quantification and 16S rRNA gene sequencing. Statistical comparisons of absolute bile acid abundance and pouch microbiota α-diversity, β-diversity, and taxa abundance were performed among the patient groups.

Results
A total of 51 samples were analyzed. Both α-diversity (P = .01, species richness) and β-diversity (P = .001) significantly differed among groups. Lithocholic acid was significantly lower in patients with chronic pouchitis/primary sclerosing cholangitis than in those with chronic pouchitis (P = .01) or normal pouch (P = .03). Decreased α-diversity was associated with an increased primary to secondary bile acid ratio (P = .002), which was also associated with changes in β-diversity (P = .006).

Conclusions
Pouch microbiota α- and β-diversity differed among patients with normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis. Lithocholic acid level and primary to secondary bile acid ratio were highly associated with pouch microbiota richness, structure, and composition. These findings emphasize the associations between pouch microbiota and bile acid composition in dysbiosis and altered metabolism, suggesting that secondary bile acids are decreased in chronic pouchitis.
Analyzing inexact hypergradients for bilevel learning
Authors: Ehrhardt Matthias J , Roberts Lindon 
Published: December 2023

Abstract
Estimating hyperparameters has been a long-standing problem in machine learning. We consider the case where the task at hand is modeled as the solution to an optimization problem. Here the exact gradient with respect to the hyperparameters cannot be feasibly computed and approximate strategies are required. We introduce a unified framework for computing hypergradients that generalizes existing methods based on the implicit function theorem and automatic differentiation/backpropagation, showing that these two seemingly disparate approaches are actually tightly connected. Our framework is extremely flexible, allowing its subproblems to be solved with any suitable method, to any degree of accuracy. We derive a priori and computable a posteriori error bounds for all our methods and numerically show that our a posteriori bounds are usually more accurate. Our numerical results also show that, surprisingly, for efficient bilevel optimization, the choice of hypergradient algorithm is at least as important as the choice of lower-level solver.
Chloroplast Genome Sequences and Phylogenetic Analysis of Eight Newly Sequenced Caryophyllaceae Species
Authors: Liu Rongpeng , Mu Zejing , Du Xiaolang , Zhong Guoyue , Wang Xiaoyun 
Published: December 2023

Abstract

Background
Caryophyllaceae is a big family composed of many economic and medicinal species. However, the phylogeny of the family is insufficient and genome data are lacking for many species.

Objective
Using next-generation sequencing (NGS) to acquire the chloroplast (cp) genomes of Eremogone acicularis (F.N.Williams) Ikonn., E. brevipetala (Tsui & L.H.Zhou) Sadeghian & Zarre, E. bryophylla (Fernald) Pusalkar & D.K.Singh, E. kansuensis (Maxim.) Dillenb. & Kadereit, Shivparvatia glanduligera (Edgew.) Pusalkar & D.K.Singh, Silene atsaensis (Marq.) Bocquet, S. caespitella Williams, and S. lhassana (Williams) Majumdar.

Methods
Bioinformatic software was used to conduct the comparative genome and phylogeny analysis of these cp genomes.

Results
The eight cp genomes were 132 188–151 919 bp in length, containing 130–132 genes. A/T was dominant in simple sequence repeats (SSRs). Forward repeats and palindromic repeats were the most frequent in long terminal repeats (LTRs). Compared with the four species of Eremogone Fenzl, the inverted repeat (IR) boundaries of S. caespitella, S. atsaensis, S. lhassana, and Sh. glanduligera were significantly expanded. Four and one mutational hotspots were identified in the large single copy (LSC) region and small single copy (SSC) region, respectively. The ratio of nonsynonymous substitution to synonymous substitution (Ka/Ks ratio) showed these cp genomes may have undergone strong purifying selection. In the phylogenetic trees, both Silene L. and Eremogone were monophyletic groups. However, Sh. glanduligera was closely related to Amaranthus hypochondriacus.

Conclusion
These results have provided new evidence and useful information for species identification, evolution, and genetic research on the Caryophyllaceae.

Highlights
In this study, eight newly sequenced cp genomes of Caryophyllaceae species were reported for the first time.
Accuracy of enteric methane emission models for cattle in sub-Saharan Africa: status quo and the way forward
Authors: Bateki Christian A , Wilkes Andreas , Schlecht Eva 
Published: December 2023

Abstract
Cattle emit over 65% of enteric methane (CH4) in sub-Saharan Africa (SSA), making them the focus of many mitigation strategies targeting livestock emissions. Since measured feed intake data are sparse, emission factors for enteric CH4 (EFCH4) are mainly estimated indirectly from gross energy intake (GEI) using the net energy (NE) requirements for different metabolic processes in cattle. However, all NE requirement systems commonly used for cattle in SSA were developed for cattle in temperate regions. Therefore, we assessed the suitability of different enteric CH4 models for estimating the GEI of cattle in SSA. The Intergovernmental Panel on Climate Change (IPCC) and South African models were identified as the main tier 2-based methods used to estimate enteric CH4 emissions from cattle in SSA. In the IPCC model, EFCH4 was estimated as (GEI * [Ym/100])/55.65, where Ym is the conversion factor (%) of gross energy in feed to CH4 and 55.65 the energy content of CH4 (MJ/kg). The GEI was estimated based on NE requirements for different metabolic processes in cattle as per the American National Research Council. In the South African model, EFCH4 was estimated as (Y/100 * GEI/55.22), where Y is the CH4 yield and 55.22 is the energy content of CH4; Y was calculated from the dry matter (DM) digestibility while GEI was calculated by predicting DM intake and multiplying it by 18.4 MJ (gross energy per kilogram DM). Also, the suitability of the British and German NE requirement systems was assessed as alternatives used for cattle nutrition in SSA. These NE systems were implemented in the IPCC model to yield the “AFRC” and “GfE” models, respectively. The four models were then evaluated using an evaluation dataset summarizing feed quality and DM intake results from 21 studies conducted in SSA, with 125 dietary treatments, and 822 cattle observations. The relative prediction error (RPE) and concordance correlation coefficient (CCC) were used to evaluate the models’ accuracy. Only the South African model estimated the GEI in dairy cattle with an acceptable RPE (18.9%) and highest CCC (0.87), while the other three models yielded estimates with RPE &gt; 20%. None of the four models we assessed estimated GEI for other cattle (i.e., nondairy) with an RPE &lt; 20% or CCC &gt; 0.30. The inaccuracy in GEI estimates suggests an error of the same magnitude in EFCH4 estimates. Therefore, a concerted effort is needed to improve the accuracy of enteric CH4 estimation models for cattle in SSA.
Inpatient Screening, Brief Intervention, and Referral to Treatment for Alcohol Use Disorder in Patients Admitted with Alcohol-associated Liver Disease Is Not Universally Implemented in Practice, But Can Reduce Readmissions for Alcohol-associated Hepatitis
Authors: Wang Dennis , Puglia Marco 
Published: December 2023

Abstract

Introduction
The management of alcohol-related liver disease requires a multidisciplinary approach to treat alcohol use disorder. We aimed to determine the proportion of actively drinking patients admitted for alcohol-associated hepatitis (AAH) or decompensated alcohol-related cirrhosis (DARLC) who were offered or underwent screening, brief intervention, and referral to treatment (SBIRT) for alcohol use disorder during admission and if inpatient SBIRT is associated with reduced readmissions for alcohol-related liver disease.

Methods
We conducted a retrospective cohort study of actively drinking patients admitted to our institution from January 2017 to December 2021 with AAH or DARLC. Logistic regression was used to identify factors, such as conducting SBIRT, that were associated with 30-day and 90-day readmissions for recurrent AAH or DARLC.

Results
There were 120 AAH admissions (mean age 47.7 ± 13.6 years), and 177 DARLC admissions (mean age 58.2 ± 9.5 years). SBIRT was conducted in only 51.7% of AAH admissions, and 23.7% of DARLC admissions. For AAH, conducting SBIRT was associated with significantly reduced 30-day (OR 0.098, P = 0.001, 95% CI 0.024–0.408) and 90-day (OR 0.166, P = 0.003, 95% CI 0.052–0.534) readmissions. For DARLC, there was no association between conducting SBIRT and 30-day or 90-day readmissions.

Conclusion
SBIRT was conducted with actively drinking patients in only 51.7% of AAH admissions and 23.7% of DARLC admissions. Patients admitted for AAH who received inpatient SBIRT had decreased 30-day and 90-day readmission rates for AAH or DARLC.
Exploring the cross-cancer effect of circulating proteins and discovering potential intervention targets for 13 site-specific cancers
Authors: Sun Jing , Luo Jia , Jiang Fangyuan , Zhao Jianhui , Zhou Siyun , Wang Lijuan , Zhang Dongfeng , Ding Yuan , Li Xue 
Published: December 2023

Abstract

Background
The proteome is an important reservoir of potential therapeutic targets for cancer. This study aimed to examine the causal associations between plasma proteins and cancer risk and to identify proteins with cross-cancer effects.

Methods
Genetic instruments for 3991 plasma proteins were extracted from a large-scale proteomic study. Summary-level data of 13 site-specific cancers were derived from publicly available datasets. Proteome-wide Mendelian randomization and colocalization analyses were used to investigate the causal effect of circulating proteins on cancers. Protein-protein interactions and druggability assessment were conducted to prioritize potential therapeutic targets. Finally, systematical Mendelian randomization analysis between healthy lifestyle factors and cancer-related proteins was conducted to identify which proteins could act as interventional targets by lifestyle changes.

Results
Genetically determined circulating levels of 58 proteins were statistically significantly associated with 7 site-specific cancers. A total of 39 proteins were prioritized by colocalization, of them, 11 proteins (ADPGK, CD86, CLSTN3, CSF2RA, CXCL10, GZMM, IL6R, NCR3, SIGLEC5, SIGLEC14, and TAPBP) were observed to have cross-cancer effects. Notably, 5 of these identified proteins (CD86, CSF2RA, CXCL10, IL6R, and TAPBP) have been targeted for drug development in cancer therapy; 8 proteins (ADPGK, CD86, CXCL10, GZMM, IL6R, SIGLEC5, SIGLEC14, TAPBP) could be modulated by healthy lifestyles.

Conclusion
Our study identified 39 circulating protein biomarkers with convincing causal evidence for 7 site-specific cancers, with 11 proteins demonstrating cross-cancer effects, and prioritized the proteins as potential intervention targets by either drugs or lifestyle changes, which provided new insights into the etiology, prevention, and treatment of cancers.
Development of local-power-free, remote α-particle detection using optical fibers
Authors: Pfeifer Kent B , Weber Thomas M , Martin James E 
Published: December 2023

Abstract
We demonstrate the application of fluorescence optical fiber coupled to a telecom grade fiber as a sensor for alpha particles using alpha-specific ZnS(Ag) scintillation materials whose wavelength is down-shifted into a low-loss region of the telecom grade fiber transmission band. Telecom-grade fiber optics offer a solution for sensing alpha radiation in deep repositories and cask storage for radioactive materials due to the stability of SiO2 under normal environmental conditions and its relative radiation hardness at low radiation doses. Long-term nuclear waste storage facilities require sensors for the detection of leakage of radioactive materials that are maintenance-free, do not require power and can survive with no ‘wear out’ mechanisms for decades. By accomplishing the wavelength transformation, we maximize efficiencies in the detection of α-particles and signal transport and can detect alpha scintillation at distances on the order of &gt;1 km with a sensor that is ~3% efficient and can be easily scaled as a sensor array. This paper describes the construction and testing of the sensor including manufacture of the controlled thickness films, verification of the wavelength shift from 450 to 620 nm and optimization of the sensitivity as a function of thickness. We also model the relative sensitivity of the film as a function of film thickness, and we demonstrate a signal-to-noise ratio of 10 at a range of greater than 1 km.
Unique cases of large and small bowel obstruction in intraperitoneal renal transplantations: a case series and review of literature
Authors: Yu Zirong , Ong Ferdinand , Kanagarajah Vijay 
Published: December 2023

Abstract
Bowel obstruction is a common cause for the acute abdomen with different aetiologies that shapes subsequent management plans. Small bowel obstruction often develop due to intra-abdominal adhesions in patients with prior abdominal surgery and for large bowel obstructions, more commonly due to tumours and lesions. Disruptions to normal intra-abdominal anatomy as seen in pancreatic–kidney transplantation or kidney transplant alone can result in increased risk of bowel obstruction—especially if the donor graft is implanted within the intraperitoneal plane. We present two patients from separate institutions with history of simultaneous pancreas–kidney (SPK) transplantation (Patient 1) and intraperitoneal renal (Patient 2) transplant whom both presented with bowel obstruction requiring surgical intervention. Given the specificity and operative intricacies of our cases, we aim to present our findings and surgical management of these rare presentations in hopes of increasing awareness to this uncommon but significant cause of bowel obstruction in a transplant patient.
Involvement of brassinosteroids and abscisic acid in spikelet degeneration in rice under soil drying during meiosis
Authors: Zhang Weiyang , Wu Mengyin , Zhong Xiaohan , Liu Ying , Yang Xinxin , Cai Wei , Zhu Kuanyu , Zhang Hao , Gu Junfei , Wang Zhiqin , Liu Lijun , Zhang Jianhua , Yang Jianchang 
Published: December 2023

Abstract
Spikelet degeneration in rice (Oryza sativa L.) is a serious physiological defect, and can be regulated by soil moisture status and phytohormones. This study investigated the possibility that brassinosteroids (BRs) in collaboration with abscisic acid (ABA) are involved in mediating the effect of soil drying during meiosis on spikelet degeneration in rice. Three rice cultivars were field grown and three irrigation regimes including well watered (WW), moderate soil drying (MD), and severe soil drying (SD) were imposed during meiosis. MD significantly decreased spikelet degeneration in comparison with WW, due mainly to the alleviation in oxidative damage via enhancing ascorbate–glutathione (AsA–GSH) cycle activity in young panicles, and SD exhibited the opposite effects. Enhanced AsA–GSH cycle strength, decreased oxidative stress, and spikelet degeneration rate were closely associated with the synergistically elevated BR and ABA levels in young panicles in MD. In contrast, low BR and excessive ABA levels led to an increase in spikelet degeneration in SD. The three cultivars exhibited the same tendencies. The intrinsic link among AsA-GSH cycle, oxidative stress, spikelet degeneration rate, and BR and ABA levels was further verified by using transgenic rice lines and chemical regulators. BRs or ABA play a unique role in regulating spikelet degeneration. Synergistically increased BR and ABA levels in MD could work together to strengthen AsA–GSH cycle activity, leading to a reduction in oxidative damage and spikelet degeneration. On the other hand, a severe imbalance between low BR and excessive ABA levels may have contributed to the opposite effects in SD.
A case of cryopyrin-associated periodic syndrome due to somatic mosaic mutation complicated with recurrent circinate erythematous psoriasis
Authors: Ando Taiki , Abe Yoshiyuki , Yamaji Ken , Nishikomori Ryuta , Tamura Naoto 
Published: December 2023

ABSTRACT
Cryopyrin-associated periotic syndrome (CAPS) is a rare autoinflammatory disease caused by genetic variants in innate immunity genes. Autoinflammatory diseases, including CAPS, mediate proinflammatory cytokines such as interleukin (IL)-1 and IL-18 and result in severe systemic inflammation. A gain-of-function mutation in the NLR family pyrin domain-containing 3 (NLRP3) gene, which encodes the protein cryopyrin, was identified to be responsible for CAPS in 2001, and since then several additional pathogenic mutations have been found. Moreover, other phenotypes have been identified based on severity and symptomatology, including familial cold autoinflammatory syndrome, Muckle–Wells syndrome, and neonatal-onset multisystem inflammatory disease/chronic neurologic cutaneous articular syndrome. Prompt diagnosis of CAPS remains challenging, however, due to unspecific, extensive clinical signs, and delayed diagnosis and treatment targeting IL-1 lead to multiorgan damage. Another factor complicating diagnosis is the existence of somatic mosaic mutations in the NLRP3 gene in some cases, resulting in symptoms and clinical courses that are atypical. The frequency of somatic mosaic mutations in CAPS was estimated to be 19% in a systematic review. Psoriasis is a chronic inflammatory skin disease that affects ∼3% of the global population. Although no reports have shown complication between CAPS and psoriasis, these diseases have several similarities and potential relationships, for instance activation of T helper 17 cells in the dermis and increased NLRP3 gene expression in psoriatic skin compared with normal skin. Here, we report a case of CAPS due to a somatic mosaic mutation with recurrent circinate erythematous psoriasis.
MAE-seq refines regulatory elements across the genome
Authors: Zhu Xiusheng , Huang Qitong , Huang Lei , Luo Jing , Li Qing , Kong Dashuai , Deng Biao , Gu Yi , Wang Xueyan , Li Chenying , Kong Siyuan , Zhang Yubo 
Published: December 2023

Abstract
Proper cell fate determination relies on precise spatial and temporal genome-wide cooperation between regulatory elements (REs) and their targeted genes. However, the lengths of REs defined using different methods vary, which indicates that there is sequence redundancy and that the context of the genome may be unintelligible. We developed a method called MAE-seq (Massive Active Enhancers by Sequencing) to experimentally identify functional REs at a 25-bp scale. In this study, MAE-seq was used to identify 626879, 541617 and 554826 25-bp enhancers in mouse embryonic stem cells (mESCs), C2C12 and HEK 293T, respectively. Using ∼1.6 trillion 25 bp DNA fragments and screening 12 billion cells, we identified 626879 as active enhancers in mESCs as an example. Comparative analysis revealed that most of the histone modification datasets were annotated by MAE-Seq loci. Furthermore, 33.85% (212195) of the identified enhancers were identified as de novo ones with no epigenetic modification. Intriguingly, distinct chromatin states dictate the requirement for dissimilar cofactors in governing novel and known enhancers. Validation results show that these 25-bp sequences could act as a functional unit, which shows identical or similar expression patterns as the previously defined larger elements, Enhanced resolution facilitated the identification of numerous cell-specific enhancers and their accurate annotation as super enhancers. Moreover, we characterized novel elements capable of augmenting gene activity. By integrating with high-resolution Hi-C data, over 55.64% of novel elements may have a distal association with different targeted genes. For example, we found that the Cdh1 gene interacts with one novel and two known REs in mESCs. The biological effects of these interactions were investigated using CRISPR-Cas9, revealing their role in coordinating Cdh1 gene expression and mESC proliferation. Our study presents an experimental approach to refine the REs at 25-bp resolution, advancing the precision of genome annotation and unveiling the underlying genome context. This novel approach not only advances our understanding of gene regulation but also opens avenues for comprehensive exploration of the genomic landscape.