bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized protocol for shotgun label-free proteomic analysis of pancreatic islets
Authors: SanchesTrevizol Juliana , Dionizio Aline , Delgado Aislan Quintiliano , Ventura Talita Mendes Oliveira , da Silva Ribeiro Caroline Fernanda , Rabelo Buzalaf Nathalia , Bosqueiro José Roberto , Buzalaf Marília Afonso Rabelo 
Published: January 2024

Abstract
Pancreatic islets are crucial in diabetes research. Consequently, this protocol aims at optimizing both the protein-extraction process and the proteomic analysis via shotgun methods for pancreatic islets. Six protocols were tested, combining three types of chemical extraction with two mechanical extraction methods. Furthermore, two protocols incorporated a surfactant to enhance enzymatic cleavage. The steps involved extraction and concentration of protein, protein quantification, reduction, alkylation, digestion, purification and desalination, sample concentration to ∼1 µl, and proteomic analysis using the mass spectrometer. The most effective protocol involves either a milder chemical extraction paired with a more intensive mechanical process, or a more robust chemical extraction paired with a gentle mechanical process, tailored to the sample’s characteristics. Additionally, it was observed that the use of a surfactant proved ineffective for these types of samples. Protocol 5 was recently used with success to examine metabolic changes in pancreatic islets of non-obese diabetic mice exposed to low doses of fluoride ions (F−) and the primary pathways altered by the treatment.
Panoramic imaging errors in machine learning model development: a systematic review
Authors: Delamare Eduardo , Fu Xingyue , Huang Zimo , Kim Jinman 
Published: January 2024

Abstract

Objectives
To investigate the management of imaging errors from panoramic radiography (PAN) datasets used in the development of machine learning (ML) models.

Methods
This systematic literature followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and used three databases. Keywords were selected from relevant literature.

Eligibility criteria
PAN studies that used ML models and mentioned image quality concerns.

Results
Out of 400 articles, 41 papers satisfied the inclusion criteria. All the studies used ML models, with 35 papers using deep learning (DL) models. PAN quality assessment was approached in 3 ways: acknowledgement and acceptance of imaging errors in the ML model, removal of low-quality radiographs from the dataset before building the model, and application of image enhancement methods prior to model development. The criteria for determining PAN image quality varied widely across studies and were prone to bias.

Conclusions
This study revealed significant inconsistencies in the management of PAN imaging errors in ML research. However, most studies agree that such errors are detrimental when building ML models. More research is needed to understand the impact of low-quality inputs on model performance. Prospective studies may streamline image quality assessment by leveraging DL models, which excel at pattern recognition tasks.
Statin treatment after surgical aortic valve replacement for aortic stenosis is associated with better long-term outcome
Authors: Pan Emily , Nielsen Susanne J , Landenhed-Smith Maya , Törngren Charlotta , Björklund Erik , Hansson Emma C , Jeppsson Anders , Martinsson Andreas 
Published: January 2024

Abstract

OBJECTIVES
The aim of this study was to evaluate the association between statin use after surgical aortic valve replacement for aortic stenosis and long-term risk for major adverse cardiovascular events (MACEs) in a large population-based, nationwide cohort.

METHODS
All patients who underwent isolated surgical aortic valve replacement due to aortic stenosis in Sweden 2006–2020 and survived 6 months after discharge were included. Individual patient data from 5 nationwide registries were merged. Primary outcome is MACE (defined as all-cause mortality, myocardial infarction or stroke). Multivariable Cox regression model adjusted for age, sex, comorbidities, valve type, operation year and secondary prevention medications is used to evaluate the association between time-updated dispense of statins and long-term outcome in the entire study population and in subgroups based on age, sex and comorbidities.

RESULTS
A total of 11 894 patients were included. Statins were dispensed to 49.8% (5918/11894) of patients at baseline, and 51.0% (874/1713) after 10 years. At baseline, 3.6% of patients were dispensed low dose, 69.4% medium dose and 27.0% high-dose statins. After adjustments, ongoing statin treatment was associated with a reduced risk for MACE [adjusted hazard ratio 0.77 (95% confidence interval 0.71–0.83). P &lt; 0.001], mainly driven by a reduction in all-cause mortality [adjusted hazard ratio, 0.70 (0.64–0.76)], P &lt; 0.001. The results were consistent in all subgroups.

CONCLUSIONS
The results suggest that statin therapy might be beneficial for patients undergoing surgical aortic valve replacement for aortic stenosis. Randomized controlled trials are warranted to establish causality between statin treatment and improved outcome.
Removal of pomt1 in zebrafish leads to loss of α-dystroglycan glycosylation and dystroglycanopathy phenotypes
Authors: Karas Brittany F , Terez Kristin R , Mowla Shorbon , Battula Namarata , Flannery Kyle P , Gural Brian M , Aboussleman Grace , Mubin Numa , Manzini M Chiara 
Published: January 2024

Abstract
Biallelic mutations in Protein O-mannosyltransferase 1 (POMT1) are among the most common causes of a severe group of congenital muscular dystrophies (CMDs) known as dystroglycanopathies. POMT1 is a glycosyltransferase responsible for the attachment of a functional glycan mediating interactions between the transmembrane glycoprotein dystroglycan and its binding partners in the extracellular matrix (ECM). Disruptions in these cell-ECM interactions lead to multiple developmental defects causing brain and eye malformations in addition to CMD. Removing Pomt1 in the mouse leads to early embryonic death due to the essential role of dystroglycan during placental formation in rodents. Here, we characterized and validated a model of pomt1 loss of function in the zebrafish showing that developmental defects found in individuals affected by dystroglycanopathies can be recapitulated in the fish. We also discovered that pomt1 mRNA provided by the mother in the oocyte supports dystroglycan glycosylation during the first few weeks of development. Muscle disease, retinal synapse formation deficits, and axon guidance defects can only be uncovered during the first week post fertilization by generating knock-out embryos from knock-out mothers. Conversely, maternal pomt1 from heterozygous mothers was sufficient to sustain muscle, eye, and brain development only leading to loss of photoreceptor synapses at 30 days post fertilization. Our findings show that it is important to define the contribution of maternal mRNA while developing zebrafish models of dystroglycanopathies and that offspring generated from heterozygous and knock-out mothers can be used to differentiate the role of dystroglycan glycosylation in tissue formation and maintenance.
Developing the next-generation cancer research workforce in the National Institutes of Health Intramural Research Program
Authors: Schor Nina F 
Published: January 2024

Abstract
Although the National Institutes of Health is renowned for being the largest funder of biomedical research in the world, the research and associated career development programs on its own campuses are relatively unknown. These intramural programs provide many outstanding and programmatically unique opportunities for research-intensive careers and training in cancer biology, prevention, diagnosis, and therapeutics. Their complementary foci, structures, and review mechanisms make the extramural and intramural cancer research contributions of the National Institutes of Health the perfect partners in the quest to rid the world of cancer as we know it.
Localized pseudomembranous gastritis associated with hepatic cirrhosis and portal hypertensive gastropathy: a case report
Authors: Tran Pierre , Sai P Rama , Prasad Chaya , Parsa Cyrus 
Published: January 2024

Abstract
Pseudomembranes in the large and small intestines are common in hospitalized patients that are immunosuppressed or on certain oral antibiotics. Pseudomembranous enterocolitis, histologically characterized by volcanic-like eruption of inflammatory cellular exudate from the mucosal surface, is mainly attributed to Clostridium difficile toxins and often presents with symptomatic diarrhea. Rarely, there are case reports of similar pseudomembranous lesions limited to the stomach in the absence of intestinal involvement. In this paper, we present a case of localized pseudomembranous gastritis in a 76-year-old patient with personal history limited to prior gastrointestinal bleed, liver cirrhosis, alcohol dependence, diabetes mellitus, and hypertension who was referred to the emergency department from his primary care physician’s office due to low hemoglobin.
Post-craniotomy coronal suture diastases in a transformed lower grade glioma
Authors: Pinheiro Teresa Morais , Awan Mariam , Wroe-Wright Oliver , Ghimire Prajwal , Marchi Francesco , Elhag Ali , Lavrador José Pedro 
Published: January 2024

Abstract
Cranial suture diastases are an uncommon clinical entity, with post craniotomy diastases being a previously undescribed finding in literature to our best knowledge. Herein, we report a case of a 28-year-old adult who underwent a second-stage low-grade glioma surgery 7 months after initial surgery. This study presents coronal suture diastases adjacent to the previously performed craniotomy. After literature and pathophysiology review, we found it to be unique and that the craniotomy can resemble the mechanical stress of trauma.
Lower limb preservation in pediatric trauma: a case study of Gustilo grade IIIC fracture in a 7-year-old
Authors: Ataya Jamal , Daaboul Rawan , Alhomsi Hassan , Issa Hassan , Elewee Ahmad 
Published: January 2024

Abstract
This case report describes the intricate aspects of managing pediatric lower limb trauma. A 7-year-old patient had a severe compound fracture and significant soft tissue damage in the left lower limb, classified as Gustilo Grade IIIC. This necessitated the use of scoring systems such as the Mangled Extremity Severity Score and limb salvage index to assess the likelihood of limb preservation. Despite these high amputation risk indicators, a multidisciplinary approach has led to limb salvage surgery with internal fixation. Detailed postoperative monitoring revealed progressive recovery culminating in restored sensation, bone healing, and functional recovery. The discussion emphasizes the difficulties in deciding between limb salvage and amputation, stressing the importance of tailored care and cautious scoring system interpretation in pediatric cases. This conclusion advocates the prioritization of limb salvage in children owing to their unique healing capabilities while highlighting the need for further research to refine treatment protocols for pediatric lower limb trauma.
On the incidence of episodic accretion in Class I YSOs from VVV
Authors: Contreras Peña Carlos , Lucas Philip W , Guo Zhen , Smith Leigh 
Published: January 2024

ABSTRACT
Episodic accretion is one of the competing models to explain the observed luminosity spread in young stellar clusters. These short-lived high accretion events could also have a strong impact on planet formation. Observations of high-amplitude variability in young stellar objects (YSOs) due to large changes in the accretion rate provide direct observational evidence for episodic accretion. However, there are still uncertainties in the frequency of these events and if episodic accretion is universal among YSOs. To determine the frequency of outbursts in Class I YSOs, we built a large and robust sample of objects at this evolutionary stage, and searched for high-amplitude near-infrared (ΔKS &gt; 2 mag) variability in the VIRAC2 database of the Vista Variables in the Via Lactea survey. By complementing with near-IR (2MASS and DENIS) and mid-IR (WISE/Neo-WISE) data, we find that from ∼7000 Class I YSOs, 97 objects can be classified as eruptive variable YSOs. The duration of the outbursts vary from a few months to longer than 9 yr, and cover a similar range of amplitudes. Values of ΔKS &gt; 5 mag, however, are only observed in outbursts with duration longer than 9 yr. When considering different effects of completeness and contamination, we estimate that the incidence of episodic accretion in Class I YSOs is between 2 and 3 per cent. Finally, we determine a recurrence time-scale of long-term outbursts (a.k.a FUors) of $\tau =1.75^{+1.12}_{-0.87}$ kyr. The latter value agrees with previous estimates and is in line with the expectations of higher frequency of FUor outbursts during younger stages of evolution.
Association between P1NP value and increases in bone mineral density in patients with postmenopausal osteoporosis treated with romosozumab
Authors: Hattori Kyosuke , Kanayama Yasuhide 
Published: January 2024

ABSTRACT

Objectives
The present study aimed to investigate the effectiveness of treatment with romosozumab for 1 year and association between bone turnover markers and changes in bone mineral density (BMD) in patients with postmenopausal osteoporosis.

Methods
Participants were 53 treatment-naïve postmenopausal osteoporosis patients. Correlations of per cent changes (Δ) in lumbar (L) and total hip (TH) BMD 12 months after initiating romosozumab with baseline demographic factors and parameters of N-terminal propeptide of Type 1 collagen (P1NP) and tartrate-resistant acid phosphatase-5b at baseline and Months 1, 3, and 6 were assessed. Multiple regression analysis was performed on factors significantly correlated with ΔL-BMD and ΔTH-BMD at Month 12.

Results
ΔL-BMD and ΔTH-BMD at Month 12 were 17.5% and 8.1%, respectively. Multiple regression analysis revealed that a high P1NP value at Month 3 predicted large increases in L-BMD and TH-BMD at Month 12. High total amount of P1NP values from baseline to Month 6 was associated with large increases in L-BMD and TH-BMD at Month 12 and was most strongly correlated with the P1NP value at Month 3.

Conclusions
A high P1NP value at Month 3 predicted large increases in both L-BMD and TH-BMD at Month 12 in postmenopausal osteoporosis patients treated with romosozumab.
Firm-level financial frictions and aggregate allocative efficiency
Authors: Maurin Laurent , Wolski Marcin 
Published: January 2024

Abstract
Capitalizing on the productivity decomposition proposed by Olley and Pakes, we analyse the role of financial factors behind the relatively muted post-crisis rebound in productivity compared to previous upturns in Europe. First, we provide an Ordinary Least Squares framework to decompose the index of sector-level productivity into trend and allocative efficiency components. We then extend our approach to estimate the contribution of firm-level confounders to the sector-level allocative component. Secondly, we find that financial leverage played an important role in explaining the change in aggregate productivity growth in Europe between 2004 and 2017. Thirdly, focusing on Northern and Western Europe, we show that the productivity potential could not be fully exploited due to access to credit conditions. Specifically, reducing collateral bottlenecks could more than double the effectiveness of financial leverage in spurring productivity growth in this region between 2014 and 2017.
Providing family updates: a primer for the medical trainee
Authors: Ng Isaac K S , Tan Li Feng , Kumarakulasinghe Nesaretnam Barr , Goh Wilson G W , Ngiam Nicola , Teo Desmond B 
Published: January 2024

Abstract
Providing family updates is a common clinical task for medical trainees and practitioners working in hospital settings. Good clinical communication skills are essential in clinical care as it is associated with improved patient satisfaction, understanding of condition, treatment adherence, and better overall clinical outcomes. Moreover, poor communications are often the source of medical complaints. However, while patient-centred communication skills training has generally been incorporated into clinical education, there hitherto remains inadequate training on clinical communications with patients’ families, which carry different nuances. In recent years, it is increasingly recognized that familial involvement in the care of hospitalized patients leads to better clinical and psychological outcomes. In fact, in Asian populations with more collectivistic cultures, families are generally highly involved in patient care and decision-making. Therefore, effective clinical communications and regular provision of family updates are essential to build therapeutic rapport, facilitate familial involvement in patient care, and also provide a more holistic understanding of the patient’s background and psychosocial set-up. In this article, we herein describe a seven-step understand the clinical context, gather perspectives, deliver medical information, address questions, concerns and expectations, provide tentative plans, demonstrate empathy, postcommunication reflections model as a practical guide for medical trainees and practitioners in provision of structured and effective family updates in their clinical practice.
IgA vasculitis nephritis—outcomes in adult-onset disease
Authors: Stanway James , Brown Nina , Pervez Afeera , Van de Perre Els , Tollitt James , Marketos Nikolaos , Wong Nikki , Dhaygude Ajay , Ponnusamy Arvind , O'Riordan Ed , Venning Michael , Segelmark Mårten , Morgan Matthew , Jayne David , Hamilton Patrick , Pusey Charles D , Oni Louise , Salama Alan D 
Published: January 2024

Abstract

Objectives
IgA vasculitis (IgAV) in adults has been relatively under-investigated. Since outcomes are worse in other forms of vasculitis with increasing age, we investigated the outcomes of IgAV comparing younger adults (18–34), middle-aged adults (35–64) and elderly patients (≥64 years) focusing on kidney outcomes.

Methods
We identified patients with renal biopsy-confirmed IgAV nephritis and collected data regarding clinical features and progression to end stage kidney disease (ESKD). The relationship between patient factors and ESKD was analysed by regression.

Results
We identified 202 cases, 34% aged 18–34, 43% aged 35–64 and 23% elderly (&gt;64 years). Median follow-up was 44 months. Elderly patients were more likely to present with ESKD (23.9%) compared with middle-aged (13.7%) and younger adults (2.9%) (χ2 11.6, P = 0.002). In patients with independent kidney function at biopsy, there was no difference in outcomes between age groups. Male gender, Black ethnicity, diabetes, histological evidence of chronic renal damage and estimated glomerular filtration rate &lt; 30 ml/min were risk factors for development of ESKD. In this observational study 68.3% of patients received glucocorticoids and 56.9% additional immunosuppression.

Conclusion
Elderly patients with IgAV are more likely to have ESKD at presentation, but there is no difference in renal survival between age groups, among those presenting with independent renal function. Renal impairment at biopsy is an independent risk factor for subsequent development of ESKD. There is significant variability in the timing of kidney biopsy and management of these patients among specialist centres. Young adults have outcomes more in keeping with childhood IgAV.
Thresholds for unacceptable work state in radiographic axial spondyloarthritis of four presenteeism and two clinical outcome measurement instruments
Authors: Capelusnik Dafne , Ramiro Sofia , Nikiphorou Elena , Maksymowych Walter P , Magrey Marina Nighat , Marzo-Ortega Helena , Boonen Annelies 
Published: January 2024

Abstract

Objectives
To (i) identify threshold values of presenteeism measurement instruments that reflect unacceptable work state in employed r-axSpA patients; (ii) determine whether those thresholds accurately predict future adverse work outcomes (AWO) (sick leave or short/long-term disability); (iii) evaluate the performance of traditional health-outcomes for r-axSpA; and (iv) explore whether thresholds are stable across contextual factors.

Methods
Data from the multinational AS-PROSE study was used. Thresholds to determine whether patients consider themselves in an ‘unacceptable work state’ were calculated at baseline for four instruments assessing presenteeism and two health outcomes specific for r-axSpA. Different approaches derived from the receiver operating characteristic methodology were used. Validity of the optimal thresholds was tested across contextual factors and for predicting future AWO over 12 months.

Results
Of 366 working patients, 15% reported an unacceptable work state; 6% experienced at least one AWO in 12 months. Optimal thresholds were: WPAI-presenteeism ≥40 (AUC 0.85), QQ-method &lt;97 (0.76), WALS ≥0.75 (AUC 0.87), WLQ-25 ≥ 29 (AUC 0.85). BASDAI and BASFI performed similarly to the presenteeism instruments: ≥4.7 (AUC 0.82) and ≥3.5 (AUC 0.79), respectively. Thresholds for WALS and WLQ-25 were stable across contextual factors, while for all other instruments they overestimated unacceptable work state in lower educated persons. Proposed thresholds could also predict future AWO, although with lower performance, especially for QQ-method, BASDAI and BASFI.

Conclusions
Thresholds of measurement instruments for presenteeism and health status to identify unacceptable work state have been established. These thresholds can help in daily clinical practice to provide work-related support to r-axSpA patients at risk for AWO.
Aberrant mitochondrial aggregation of TDP-43 activated mitochondrial unfolded protein response and contributed to recovery of acetaminophen induced acute liver injury
Authors: Liu Zhaoxiong , Qiang Yalong , Shan Shulin , Wang Shuai , Liu Zhidan , Yang Yiyu , Huang Zhengcheng , Song Mingxue , Zhao Xiulan , Song Fuyong 
Published: January 2024

Abstract
Mitochondrial dysfunction is a key pathological event in the acute liver injury following the overdose of acetaminophen (APAP). Calpain is the calcium-dependent protease, recent studies demonstrate that it is involved in the impairment of mitochondrial dynamics. The mitochondrial unfolded protein response (UPRmt) is commonly activated in the context of mitochondrial damage following pathological insults and contributes to the maintenance of the mitochondrial quality control through regulating a wide range of gene expression. More importantly, it is reported that abnormal aggregation of TDP-43 in mitochondria induced the activation of UPRmt. However, whether it is involved in APAP induced-hepatotoxicity remains unclear. In the present study, C57/BL6 mice were given 300 mg/kg APAP to establish a time-course model of acute liver injury. Furthermore, Calpeptin, the specific inhibiter of calpains, was used to conduct the intervention experiment. Our results showed, APAP exposure produced severe liver injury. Moreover, TDP-43 was obviously accumulated within mitochondria whereas mitochondrial protease LonP1 was significantly decreased. However, these changes exhibited significant recovery at 48 h. By contrast, the mitochondrial protease ClpP and chaperone mtHSP70 and HSP60 were consistently increased, which supported the UPRmt was activated to promote protein homeostasis. Further investigation revealed that calpain-mediated cleavage of TDP-43 could promote the accumulation of TDP-43 in mitochondria compartment, thereby facilitating the activation of UPRmt. Additionally, Calpeptin pretreatment not only protected against APAP-induced liver injury, but also suppressed the formation of TDP-43 aggregates and the activation of UPRmt. Taken together, our findings indicated that in APAP-induced acute liver injury, calpain-mediated cleavage of TDP43 caused its aberrant aggregation on the mitochondria. As a stress-protective response, the induction of UPRmt contributed to the recovery of mitochondrial function.