bluuebunny/crossref_metadata_2025_split huggingface dataset:
PGPointNovo: an efficient neural network-based tool for parallel de novo peptide sequencing
Authors: Xu Xiaofang , Yang Chunde , He Qiang , Shu Kunxian , Xinpu Yuan , Chen Zhiguang , Zhu Yunping , Chen Tao 
Published: April 2023

Abstract

Summary
De novo peptide sequencing for tandem mass spectrometry data is not only a key technology for novel peptide identification, but also a precedent task for many downstream tasks, such as vaccine and antibody studies. In recent years, neural network models for de novo peptide sequencing have manifested a remarkable ability to accommodate various data sources and outperformed conventional peptide identification tools. However, the excellent model is computationally expensive, taking up to 1 week to process about 400 000 spectrums. This article presents PGPointNovo, a novel neural network-based tool for parallel de novo peptide sequencing. PGPointNovo uses data parallelization technology to accelerate training and inference and optimizes the training obstacles caused by large batch sizes. The results of extensive experiments conducted on multiple datasets of different sizes demonstrate that compared with PointNovo the excellent neural network-based de novo peptide sequencing tool, PGPointNovo, accelerates de novo peptide sequencing by up to 7.35× without precision or recall compromises.

Availability and implementation
The source code and the parameter settings are available at https://github.com/shallFun4Learning/PGPointNovo.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
“Beyond BAME, WOC, and ‘political blackness’”: diasporic digital communing practices
Authors: Sobande Francesca , Basu Maitrayee 
Published: April 2023

Abstract
What forms of opacity and excess propel Black and South Asian digital diasporic feminist cultures of commoning and communing? This article explores digital expressions of retreat, refusal, remixing, and reclamation which are central to diasporic feminist practices. We analyze three illustrative digital practices via two vignettes: (1) Quote tweets and digital anonymity as expressions of subaltern excess; (2) diasporic meme culture as a callout praxis of refusal; and (3) digital opacity as feminist retreat and reclamation of time, interiority, and intimacy. Throughout our analysis we incorporate reflections on the contours of “diasporic feminist excess” and the parameters of public, private, and personal spaces. Overall, by extending the vocabularies of feminist commoning to include certain digital diasporic feminist practices, we conceptualize the fluid and fraught ways that contrapublic discourses move in, between, and beyond, digital publics.
Threading the needle: a case report of double-wiring technique and double intracoronary imaging guidance for a multifenestrated iatrogenic coronary artery dissection
Authors: Viegas José Miguel , Ferreira Vera , Pereira-da-Silva Tiago , Ferreira Rui Cruz 
Published: April 2023

Abstract

Background
Iatrogenic coronary artery dissection (ICAD) may represent a serious complication of percutaneous coronary intervention. Stenting the dissected segment is recommended in large dissections with compromised distal blood flow, although wiring the true lumen is often difficult.

Case summary
A 64-year-old woman with effort angina was submitted to invasive coronary angiography that revealed a severe stenosis in the distal right coronary artery. A large spiral ICAD occurred after pre-dilatation and guidewire position is lost. We report the treatment of this multifenestrated dissection using combined intracoronary imaging guidance with angiographic co-registered optical coherence tomography and real-time intravascular ultrasound, which were crucial to achieve a successful outcome.

Discussion
A double-wiring technique with double intracoronary imaging guidance enables a comprehensive depiction of the compromised artery and should be considered in selected cases to guide true lumen wiring and stent implantation.
Tomato LysM receptor kinase 4 mediates chitin-elicited fungal resistance in both leaves and fruit
Authors: Ai Yingfei , Li Qinghong , Li Chenying , Wang Ran , Sun Xun , Chen Songyu , Cai Xin-Zhong , Qi Xingjiang , Liang Yan 
Published: April 2023

Abstract
Fungal infection is a major cause of crop and fruit losses. Recognition of chitin, a component of fungal cell walls, endows plants with enhanced fungal resistance. Here, we found that mutation of tomato LysM receptor kinase 4 (SlLYK4) and chitin elicitor receptor kinase 1 (SlCERK1) impaired chitin-induced immune responses in tomato leaves. Compared with the wild type, sllyk4 and slcerk1 mutant leaves were more susceptible to Botrytis cinerea (gray mold). SlLYK4 extracellular domain showed strong binding affinity to chitin, and the binding of SlLYK4 induced SlLYK4-SlCERK1 association. Remarkably, qRT–PCR analysis indicated that SlLYK4 was highly expressed in tomato fruit, and β-GLUCURONIDASE (GUS) expression driven by the SlLYK4 promoter was observed in tomato fruit. Furthermore, SlLYK4 overexpression enhanced disease resistance not only in leaves but also in fruit. Our study suggests that chitin-mediated immunity plays a role in fruit, providing a possible way to reduce fungal infection-related fruit losses by enhancing the chitin-induced immune responses.
EuMAR: a roadmap towards a prospective, cycle-by-cycle registry of medically assisted reproduction in Europe
Authors: De Geyter Christian , Calhaz-Jorge Carlos , Goossens Veerle , Magli Cristina M , Smeenk Jesper , Vesela Kristina , Vermeulen Nathalie , Wyns Christine 
Published: April 2023

ABSTRACT
More than 20 years ago, the survey of activities in medically assisted reproduction (MAR) was initiated in Europe and resulted in cross-sectional annual reports, as issued by the European IVF Monitoring (EIM) consortium of ESHRE. Over time, these reports mirror the continuous development of the technologies and contribute to increased transparency and surveillance of reproductive care. Meanwhile, progressive changes of existing treatment modalities and the introduction of new technologies resulted in the need of a cumulative approach in the assessment of treatment outcomes, which warrants a prospective cycle-by-cycle data registry on MAR activities, including fertility preservation. This change in the paradigm of data collection in Europe towards the construction of cumulative outcome results is expected to generate additional insights into cross-institutional but also cross-border movements of patients and reproductive material. This is essential to improve vigilance and surveillance. The European monitoring of Medically Assisted Reproduction (EuMAR) project, co-funded by the European Union, will establish a registry for the transnational collection of prospective cycle-by-cycle MAR and fertility preservation data on the basis of an individual reproductive care code (IRCC). The rationale for the project and the objectives are presented here.
Optimal control of energy storage system of high-permeability distributed photovoltaic low-voltage distribution network
Authors: Yang Yi , Yuan Yubo , Jiao Hao , Chen Jinming , Pang Xianglu , Zhuang Shuyi 
Published: April 2023

Abstract
Photovoltaic (PV) is one of the very promising renewable energy sources, but its output power is fluctuating. To maintain PV-energy storage system-load power balance in low-voltage distribution networks, we propose a new optimized sag control strategy, which is no longer indexed by the battery voltage but by the battery state of charge (SOC) because the battery SOC can better reflect the remaining battery capacity for better performance. In addition, to further optimize its performance, we try to use the ratio of intercell SOC for optimization. We analysed the deficiencies of sag control in detail, derived a control strategy with cell SOC as an indicator and finally analysed its performance in detail. To verify the performance of the proposed strategy, based on MATLAB, we designed the power variation of 2 lithium-ion battery packs to maintain the bus power stability under two cases of sudden rise as well as sudden fall of PV power and 3 lithium-ion battery packs to maintain during the bus power stabilization with one set of performance after failure, and the simulation results prove the feasibility of the proposed strategy.
Measuring health system responsiveness in a national community health worker primary care programme in rural Liberia
Authors: Mendin Savior Flomo , Krause Julie A , Gweh Andrew , Baysah Massaboi , Nyumah Joseph , Gaye Chris J , Max Zorh T- , Kraemer John D , Subah Marion , Hirschhorn Lisa R 
Published: April 2023

Abstract
As many low- and middle-income countries scale up community health worker (CHW) programmes to achieve universal health coverage, ensuring quality as well as access is critical. Health system responsiveness (HSR) is a core domain of quality patient-centred care but has not been widely measured in CHW-delivered care. We report results from a household survey measuring HSR and health systems’ quality of CHW-delivered care in two Liberian counties where the national CHW programme of Community Health Assistants (CHAs) for communities ≥5 km from a health centre has been implemented. We conducted a cross-sectional population-based household survey in 2019 in Rivercess (RC) and Grand Gedeh (GG) counties, using a two-stage cross-sectional cluster sampling approach. We included validated HSR questions on six responsiveness domains and patient-reported health system outcomes, such as satisfaction and trust in the CHA’s skills and abilities. The HSR questions were administered to women aged 18–49 years who reported seeking care from a CHA in the 3 months prior to the survey. A composite responsiveness score was calculated and divided into tertiles. Multivariable analysis using Poisson regression with log link and adjusting for respondent characteristics was used to determine the association between responsiveness and patient-reported health system outcomes. The proportion of individuals rating responsiveness as very good or excellent was similar across all domains within a district, with ratings being lower in RC (23–29%) than in GG (52–59%). High ratings in both counties were seen for high trust in the CHA’s skills and abilities (GG 84%, RC 75%) and high confidence in the CHA (GG 58%, RC 60%). Compared with women in the lowest responsiveness tertile (score ≤3), women in the highest tertile (score $ \ge $4.25) were significantly more likely to report high quality of CHA-delivered care (prevalence ratio, PR = 14.1), very good/excellent at meeting health needs (PR = 8.0), high confidence in the CHA to provide future care (PR = 2.4), and a high level of trust in CHA’s skills and abilities (PR = 1.4). Controlling for respondent characteristics, the composite responsiveness score was significantly associated with all patient-reported health system outcomes (P &lt; 0.001). We found that HSR was associated with important patient-reported health system quality outcomes, including satisfaction, trust, and confidence in the CHA. Measuring patients’ experience and outcomes of care is important to complement more common measures of technical quality for CHW-delivered care to ensure that this domain of quality is central to the community health programme design and delivery.
Utility of indocyanine green in assessing blood perfusion in anomalous systemic arterial supply to the lung
Authors: Kumeda Hirotaka , Saito Gaku 
Published: April 2023

Abstract
The chosen treatment for anomalous systemic arterial supply to the basal segment of the lung (ABLL) is typically the division of the anomalous artery and resection of the abnormal area, dependent on the anomalous artery. Although only division or interventional embolization of the anomalous artery may be selected. However, leaving the area dependent on the anomalous artery can lead to complications, such as necrosis and pulmonary infarction. We report the case of a 39-year-old female with ABLL. Intraoperatively, the anomalous artery was first divided. Indocyanine green (ICG) was subsequently injected intravenously to evaluate blood perfusion within the abnormal lung area. Since the abnormal area was still poorly perfused after a few minutes, a left basal segmentectomy was performed because of the possibility of complications. Thus, evaluation of perfusion via ICG can be used in the decision to resect abnormal area.
The transplant ureter causing small bowel obstruction following intraperitoneal kidney transplantation: a case report
Authors: Selim Motaz A , Krepline Ashley , Eriksen Calvin , Murphy Patrick , Cooper Matthew 
Published: April 2023

Abstract
Internal bowel herniation under the ureter of an intraperitoneally transplanted kidney is a rare complication yet carries a high burden of morbidity and potential mortality if not recognized and managed appropriately. We describe a case where early intervention salvaged the bowel without ureteral injury. We also describe a technique to close the space beneath the ureter to prevent further episodes of internal herniation.
Symptoms of illness during travel and risk factors for non-adherence to malaria prophylaxis—a cross-sectional study in travellers from Germany
Authors: Reinsberg Friederike , Moehlmann Mary W , Krumkamp Ralf , Landsmann Lena , Heitkamp Christian , Jochum Johannes , Addo Marylyn , Ramharter Michael , Radt Christiane , Rothe Camilla , Vinnemeier Christof , Kreuels Benno 
Published: April 2023

Abstract

Background
Perceived adverse effects of antimalarial chemoprophylaxis can be difficult to distinguish from travel-related illness and are often cited as important reasons for non-adherence or refusal of antimalarial chemoprophylaxis. We aimed to investigate the occurrence of symptoms of illness in travellers with and without chemoprophylaxis in a cross-sectional study after travel and to identify risk factors for non-adherence to prophylaxis.

Methods
We enrolled 458 travellers to Africa and South America during their pre-travel medical consultation at the travel clinic of the University Medical Centre Hamburg-Eppendorf and conducted post-travel interviews on symptoms of illness and intake of malaria prophylaxis.

Results
Eleven percent (49/437) of the participants reported symptoms of illness during travel. In total, 36% (160/448) of the participants reported prescription of chemoprophylaxis, the vast majority of these travelled to Africa (98%) and received atovaquone/proguanil (93%). Frequency of symptoms did not differ significantly between participants without prophylaxis and those taking atovaquone/proguanil. Non-adherence to prophylaxis was frequent (20%), but only 3% (4/149) of the participants stopped the medication early because of perceived side effects. Risk factors associated with non-adherence to prophylaxis included age under 30 years, travel to West or Central Africa and travel duration greater than 14 days.

Conclusions
Symptoms of illness during travel occurred at similar frequencies irrespective of intake of chemoprophylaxis. Travellers should be informed about chemoprophylaxis in a balanced way, without raising fear of side effects, especially among groups at higher risk for incorrect use of prophylaxis.
Melting of Fe-bearing and Fe-free carbonated pelites under fluid-saturated conditions at 6 GPa
Authors: Chen Xueqian , Wang Meili , Inoue Toru , Liu Qiong , Zhang Lifei 
Published: April 2023

Abstract
Although the induced melting of pelitic sediments, i.e., the devolatilization of hydrous and carbonate minerals, has been widely studied at fluid-undersaturated conditions, the flush dissolution of carbonated pelite has not been fully understood. In addition, the role of iron in the melting of carbonated pelite has not received much attention. To address these issues, we conducted two sets of experiments for carbonated pelite with an iron-bearing (LH-gloss) and an iron-free (LHIF-gloss) starting bulk composition at 5.5 to 6 GPa, 800 to 1600 °C at fluid-saturated conditions. The phase assemblages for both experiments at 800 °C are composed of garnet + clinopyroxene + coesite + kyanite + phengite + aragonite + magnesite ± lawsonite ± rutile. Higher jadeite component and lower diopside–hedenbergite solid solution (Di–Hdss) in omphacitic clinopyroxene are observed in the LH-gloss experiments; also, garnet remains stable to higher temperatures (800–1400 °C) in the LH-gloss than in the LHIF-gloss (900–1200 °C). Carbonate- and phengite-out temperature boundaries are overlapping in the respective system, with the temperature boundary in the LH-gloss (800–900 °C) slightly lower than that in the LHIF-gloss experiments (900–1000 °C). The different stability fields of volatile-bearing minerals can be ascribed not only to variable bulk XH2O [molar ratio H2O/(H2O + CO2)], which in turn depends on bulk H2O, CO2 and K2O contents, but also to bulk FeO*(Total Fe as FeO) content. Both the characteristic “fish egg” texture and the strong increase in the amount of dissolved solids in the liquid phase over a narrow temperature interval at 6 GPa testify to the possible existence of supercritical fluid. The marked solvent power of supercritical fluid can explain the earlier disappearance of experimental products including phengite, aragonite and magnesite. For the produced liquid phase (supercritical fluid or melt), the K2O/Na2O weight ratio decreases, whereas that of the SiO2/CaO increases with increasing temperature, placing potassium-rich carbonatitic supercritical fluids in the low-temperature and sodium-rich (carbonated) silicate melts in the high-temperature sections of both systems. The produced ultrapotassic (supercritical) liquid, when liberated from the subducting slab, may evolve into a melt parental to carbonatites and possibly result in the formation of diamonds. While those (carbonated) silicate melts, especially the more oxidized and buoyant ones produced by the melting of ferrous iron-depleted carbonated pelite, are expected to intensely interact with the overlying peridotite during the upward migration, which could lead to the formation of the metasomatic garnet pyroxenite.
Developmental pyrethroid exposure causes a neurodevelopmental disorder phenotype in mice
Authors: Curtis Melissa A , Dhamsania Rohan K , Branco Rachel C , Guo Ji-Dong , Creeden Justin , Neifer Kari L , Black Carlie A , Winokur Emily J , Andari Elissar , Dias Brian G , Liu Robert C , Gourley Shannon L , Miller Gary W , Burkett James P 
Published: April 2023

AbstractNeurodevelopmental disorders (NDDs) are a widespread and growing public health challenge, affecting as many as 17% of children in the United States. Recent epidemiological studies have implicated ambient exposure to pyrethroid pesticides during pregnancy in the risk for NDDs in the unborn child. Using a litter-based, independent discovery–replication cohort design, we exposed mouse dams orally during pregnancy and lactation to the Environmental Protection Agency's reference pyrethroid, deltamethrin, at 3 mg/kg, a concentration well below the benchmark dose used for regulatory guidance. The resulting offspring were tested using behavioral and molecular methods targeting behavioral phenotypes relevant to autism and NDD, as well as changes to the striatal dopamine system. Low-dose developmental exposure to the pyrethroid deltamethrin (DPE) decreased pup vocalizations, increased repetitive behaviors, and impaired both fear conditioning and operant conditioning. Compared with control mice, DPE mice had greater total striatal dopamine, dopamine metabolites, and stimulated dopamine release, but no difference in vesicular dopamine capacity or protein markers of dopamine vesicles. Dopamine transporter protein levels were increased in DPE mice, but not temporal dopamine reuptake. Striatal medium spiny neurons showed changes in electrophysiological properties consistent with a compensatory decrease in neuronal excitability. Combined with previous findings, these results implicate DPE as a direct cause of an NDD-relevant behavioral phenotype and striatal dopamine dysfunction in mice and implicate the cytosolic compartment as the location of excess striatal dopamine.
Live and carcass production traits for progeny of purebred sires in comparison with the clone of a USDA prime yield grade one carcass
Authors: Sperber Jessica L , Lust David G , Veneklasen Gregg O , Hawkins Dean E , McEvers Trent J , Lawrence Ty E 
Published: April 2023

Abstract
Cloning is a technology by which an animal’s tissue can be salvaged and replicated. Carcasses that grade USDA prime–yield grade 1 (P1) represent a rare and antagonistic outcome and are a goal for terminal sire selection in the United States. A terminal sire progeny test generated offspring for a crossbred bull (14% Zebu, 86% Angus; ALPHA), born in 2012 via somatic cell nuclear transfer (SCNT) from a carcass that graded P1. ALPHA progeny (steers and heifers) were compared against progeny of three purebred (Angus; Charolais; Simmental) reference sires. Live production traits included weaning weight, morbidity, mortality, and days on feed; carcass traits included abscessed liver frequency and lung lesion frequency, individual quality and yield grade (YG) parameters, and carcass value. Observed carcass traits for progeny from the Angus, Charolais, and Simmental sires were reflective of the carcass outcomes expected for each sire’s respective breed. Calves sired by the Angus were the earliest maturing indicated by the youngest chronological age at harvest (P ≤ 0.02) concomitant with the most backfat (P &lt; 0.01), and the greatest marbling scores (P &lt; 0.01). Calves sired by the Charolais had the heaviest carcass weight (P = 0.04), greatest cutability as assessed by USDA calculated YG (P &lt; 0.01) and were the heaviest muscled based on “longissimus” muscle area (P &lt; 0.01). ALPHA-sired calves were the most similar in carcass outcomes to calves sired by the Simmental, combining advantageous quality and yield parameters to produce an intermediate for carcass quality and yield. The economic value of moderate carcass outcomes is reflected in the carcass value per century weight, in which ALPHA-sired steers tended (P = 0.07) to be of the greatest value compared to other sire groups. ALPHA progeny performed comparably to high-performing reference sires for terminal sire production traits and the P1 genetics in which ALPHA was cloned have economical and biological value in modern U.S. beef production.
Intestinal transplantation: an update
Authors: Sharkey Lisa M. , Russell Neil K. 
Published: April 2023

Purpose of review
The role of intestinal transplant has expanded in recent years and is no longer only considered for patients with no other options remaining. 5 year survival in high-volume centres is over 80% for certain graft types. The aim of this review is to update the audience on the current state of intestinal transplant, with a focus on recent medical and surgical advances.

Recent findings
There has been a greater understanding of the interplay and balance of host and graft immune responses, which may facilitate individualized immunosuppression. Some centres are now performing ‘no-stoma’ transplants, with preliminary data showing no adverse effects from this strategy and other surgical advances have lessened the physiological insult of the transplant operation. Earlier referrals are encouraged by transplant centres, such that vascular access or liver disease has not progressed too much to increase the technical and physiological challenge of the procedure.

Summary
Clinicians should consider intestinal transplant as a viable option for patients with intestinal failure, benign unresectable abdominal tumours or acute abdominal catastrophes.