Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimitochondrial antibody associated with liver cirrhosis in patients with primary biliary cholangitis

Antimitochondrial antibody (AMA) serves as a serological marker for diagnosing primary biliary cholangitis (PBC). However, the association between AMA and prognosis for PBC patients remains unclear. The objective of this study was to investigate the relationship between AMA and cirrhosis in PBC patients. This retrospective study enrolled 225 PBC patients, including 127 with liver cirrhosis and 98 without cirrhosis. AMA was tested by indirect immunofluorescence (IIF) with rat kidney as the substrate. AMA-M2 and M2-3E were detected by line immunoassay (LIA). The overall positivity rate for AMA detection in PBC patients was 80.9%. The positivity rates of IIF-AMA, AMA-M2, and M2-3E were significantly higher in patients with liver cirrhosis than in those without cirrhosis (73.2% vs. 52.0%, 74.0% vs. 51.0%, and 80.3% vs. 60.2%, respectively). In multivariate logistic regression, IIF-AMA (OR: 3.05, 95% CI: 1.59–5.87), AMA-M2 (OR: 3.11, 95% CI: 1.61–6.01), and M2-3E (OR: 3.29, 95% CI: 1.63–6.66) remained significantly associated with an increased incidence of liver cirrhosis. Moreover, in multinomial logistic regression, IIF-AMA (compensated cirrhosis, OR: 3.55, 95% CI: 1.49–8.44; decompensated cirrhosis, OR: 2.86, 95% CI: 1.32–6.18), AMA-M2 (compensated cirrhosis, OR: 4.74, 95% CI: 1.94–11.58; decompensated cirrhosis, OR: 2.51, 95% CI: 1.19–5.33), and M2-3E (compensated cirrhosis, OR: 4.92, 95% CI: 1.74–13.96; decompensated cirrhosis, OR: 2.91, 95% CI: 1.28–6.64) were all found to be associated with different stages of liver cirrhosis. AMA was found to be associated with the occurrence of liver cirrhosis in PBC patients. Additionally, AMA was also related to different stages of liver cirrhosis, including compensated and decompensated cirrhosis.
The spectrum of gastrointestinal functional bowel disorders in joint hypermobility syndrome and in an academic referral center

Joint hypermobility syndrome (JHS) is a non-inflammatory hereditary disorder of connective tissue with varied clinical presentations, including frequent joint dislocations, hyperextensible skin, easy bruising, and abnormal paper-thin scar formation. Many of these patients have unexplained gastrointestinal (GI) symptoms. Our aim was to evaluate the prevalence of JHS in a tertiary gastroenterology motility clinic and the spectrum of functional bowel disorders in JHS patients. In this retrospective case series, we screened the medical records of 277 patients seen over 4 years at an academic GI Motility Center. The patients who met the criteria for JHS by Beighton hypermobility score were evaluated for the presence of functional GI disorders by Rome IV criteria. They also underwent gastric emptying study and glucose breath testing for small intestinal bacterial overgrowth. The prevalence of JHS in the study population was 9.7%. The mean age was 27 years, and 92.5% were female. The symptoms experienced by these patients include nausea/vomiting (89%), abdominal pain (70%), constipation (48%), and bloating (18.5%). The disorders associated with JHS include gastroparesis (52%), irritable bowel syndrome (55.5%), and gastroesophageal reflux disease (30%). Also, 10 patients (37%) were diagnosed with postural hypotension tachycardia syndrome secondary to autonomic dysfunction. Approximately 10% of patients with suspected functional bowel disorders have hypermobility syndrome. Hence, it is crucial to familiarize gastrointestinal practitioners with the criteria utilized to diagnose JHS and the methods to identify physical examination findings related to this condition.
Plasma cell‐free DNA methylation analysis for ovarian cancer detection: Analysis of samples from a case‐control study and an ovarian cancer screening trial

Analysis of cell‐free DNA methylation (cfDNAme), alone or combined with CA125, could help to detect ovarian cancers earlier and may reduce mortality. We assessed cfDNAme in regions of ZNF154, C2CD4D and WNT6 via targeted bisulfite sequencing in diagnostic and early detection (preceding diagnosis) settings. Diagnostic samples were obtained via prospective blood collection in cell‐free DNA tubes in a convenience series of patients with a pelvic mass. Early detection samples were matched case‐control samples derived from the UK Familial Ovarian Cancer Screening Study (UKFOCSS). In the diagnostic set (ncases = 27, ncontrols = 41), the specificity of cfDNAme was 97.6% (95% CI: 87.1%‐99.9%). High‐risk cancers were detected with a sensitivity of 80% (56.3%‐94.3%). Combination of cfDNAme and CA125 resulted in a sensitivity of 94.4% (72.7%‐99.9%) for high‐risk cancers. Despite technical issues in the early detection set (ncases = 29, ncontrols = 29), the specificity of cfDNAme was 100% (88.1%‐100.0%). We detected 27.3% (6.0%‐61.0%) of high‐risk cases with relatively lower genomic DNA (gDNA) contamination. The sensitivity rose to 33.3% (7.5%‐70.1%) in samples taken <1 year before diagnosis. We detected ovarian cancer in several patients up to 1 year before diagnosis despite technical limitations associated with archival samples (UKFOCSS). Combined cfDNAme and CA125 assessment may improve ovarian cancer screening in high‐risk populations, but future large‐scale prospective studies will be required to validate current findings.
The Association of Polish Surgeons (APS) clinical guidelines for the use of laparoscopy in the management of abdominal emergencies. Part II

Introduction Over the past three decades, almost every type of abdominal surgery has been performed and refined using the laparoscopic technique. Surgeons are applying it for more procedures, which not so long ago were performed only in the classical way. The position of laparoscopic surgery is therefore well established, and in many operations it is currently the recommended and dominant method. Aim The aim of the preparation of these guidelines was to concisely summarize the current knowledge on laparoscopy in acute abdominal diseases for the purposes of the continuous training of surgeons and to create a reference for opinions. Material and methods The development of these recommendations is based on a review of the available literature from the PubMed, Medline, EMBASE and Cochrane Library databases from 1985 to 2022, with particular emphasis on systematic reviews and clinical recommendations of recognized scientific societies. The recommendations were formulated in a directive form and evaluated by a group of experts using the Delphi method. Results and conclusions There are 63 recommendations divided into 12 sections: diagnostic laparoscopy, perforated ulcer, acute pancreatitis, incarcerated hernia, acute cholecystitis, acute appendicitis, acute mesenteric ischemia, abdominal trauma, bowel obstruction, diverticulitis, laparoscopy in pregnancy, and postoperative complications requiring emergency surgery. Each recommendation was supported by scientific evidence and supplemented with expert comments. The guidelines were created on the initiative of the Videosurgery Chapter of the Association of Polish Surgeons and are recommended by the national consultant in the field of general surgery. The second part of the guidelines covers sections 6 to12 and the following challenges for surgical practice: acute appendicitis, acute mesenteric ischemia, abdominal injuries, bowel obstruction, diverticulitis, laparoscopy in pregnancy and postoperative complications requiring a reoperation.
Antiepileptic treatment with levetiracetam during the first trimester and pregnancy outcome: An observational study

Levetiracetam is increasingly used in pregnant women with epilepsy. Although teratogenic effects have not been observed so far, data on the risks of spontaneous abortion and major birth defects are still limited, especially for the frequently used dual therapy of levetiracetam and lamotrigine. Our primary aim was to analyze rates of major birth defects and spontaneous abortion after maternal levetiracetam treatment.
The Gram-negative permeability barrier: tipping the balance of the in and the out

ABSTRACT Gram-negative bacteria are intrinsically resistant to many antibiotics, due in large part to the permeability barrier formed by their cell envelope. The complex and synergistic interplay of the two Gram-negative membranes and active efflux prevents the accumulation of a diverse range of compounds that are effective against Gram-positive bacteria. A lack of detailed information on how components of the cell envelope contribute to this has been identified as a key barrier to the rational development of new antibiotics with efficacy against Gram-negative species. This review describes the current understanding of the role of the different components of the Gram-negative cell envelope in preventing compound accumulation and the state of efforts to describe properties that allow compounds to overcome this barrier and apply them to the development of new broad-spectrum antibiotics.
A Network of Field Sites for Reactive Soil Monitoring in the Newcastle-Hunter Region

A network of twenty field sites has been established in the Newcastle-Hunter region of New South Wales to allow long term monitoring of ground movements and soil moisture profiles associated with reactive soils. The sites cover a range of soil, geological and geographic conditions and have been located in areas designated for future residential development. Instrumentation allows surface and sub-surface movements and moisture profiles to be recorded on a monthly basis to depths up to 3m. This paper details the site selection, establishment, instrumentation and laboratory testing and presents preliminary ground movement, soil moisture and laboratory data. Site monitoring began in July 1994 and initial results indicate a wide range of ground movements throughout the region as well as site specific variation. Preliminary ground movements are compared to those predicted on the basis of laboratory index tests.
Multifaceted TGF‐β signaling, a master regulator: From bench‐to‐bedside, intricacies, and complexities

Physiological embryogenesis and adult tissue homeostasis are regulated by transforming growth factor‐β (TGF‐β), an evolutionarily conserved family of secreted polypeptide factors, acting in an autocrine and paracrine manner. The role of TGF‐β in inflammation, fibrosis, and cancer is complex and sometimes even contradictory, exhibiting either inhibitory or promoting effects depending on the stage of the disease. Under pathological conditions, especially fibrosis and cancer, overexpressed TGF‐β causes extracellular matrix deposition, epithelial–mesenchymal transition, cancer‐associated fibroblast formation, and/or angiogenesis. In this review article, we have tried to dive deep into the mechanism of action of TGF‐β in inflammation, fibrosis, and carcinogenesis. As TGF‐β and its downstream signaling mechanism are implicated in fibrosis and carcinogenesis blocking this signaling mechanism appears to be a promising avenue. However, targeting TGF‐β carries substantial risk as this pathway is implicated in multiple homeostatic processes and is also known to have tumor‐suppressor functions. There is a need for careful dosing of TGF‐β drugs for therapeutic use and patient selection.
Very long period conduit oscillations induced by rockfalls at Kilauea Volcano, Hawaii

Eruptive activity at the summit of Kilauea Volcano, Hawaii, beginning in 2010 and continuing to the present time is characterized by transient outgassing bursts accompanied by very long period (VLP) seismic signals triggered by rockfalls from the vent walls impacting a lava lake in a pit within the Halemaumau pit crater. We use raw data recorded with an 11‐station broadband network to model the source mechanism of signals accompanying two large rockfalls on 29 August 2012 and two smaller average rockfalls obtained by stacking over all events with similar waveforms to improve the signal‐to‐noise ratio. To determine the source centroid location and source mechanism, we minimize the residual error between data and synthetics calculated by the finite difference method for a point source embedded in a homogeneous medium that takes topography into account. We apply a new waveform inversion method that accounts for the contributions from both translation and tilt in horizontal seismograms through the use of Green's functions representing the seismometer response to translation and tilt ground motions. This method enables a robust description of the source mechanism over the period range 1–1000 s. The VLP signals associated with the rockfalls originate in a source region ∼1 km below the eastern perimeter of the Halemaumau pit crater. The observed waveforms are well explained by a simple volumetric source with geometry composed of two intersecting cracks including an east striking crack (dike) dipping 80° to the north, intersecting a north striking crack (another dike) dipping 65° to the east. Each rockfall is marked by a similar step‐like inflation trailed by decaying oscillations of the volumetric source, attributed to the efficient coupling at the source centroid location of the pressure and momentum changes induced by the rock mass impacting the top of the lava column. Assuming a simple lumped parameter representation of the shallow magmatic system, the observed pressure and volume variations can be modeled with the following attributes: rockfall volume (200–4500 m3), length of magma column (120–210 m), diameter of pipe connecting the Halemaumau pit crater to the subjacent dike system (6 m), average thickness of the two underlying dikes (3–6 m), and effective magma viscosity (30–210 Pa s). Most rockfalls occur during episodes of sustained deflation of the Kilauea summit. The mass loss rate in the shallow magmatic system is estimated to be 1400–15,000 kg s−1 based on measurements of the temporal variation of VLP period in the two large rockfalls that occurred on 29 August 2012.
Disease-modifying effect and long-term safety of belimumab in patients with systemic lupus erythematosus: A single-center retrospective study

Background Disease modification in systemic lupus erythematosus (SLE) is important for minimizing disease activity while limiting treatment-associated toxicities. Belimumab can be used as a remission-induction/maintenance systemic lupus erythematosus therapy; however, its disease-modifying effects are unclear. We aimed to determine these effects in patients with systemic lupus erythematosus. Methods This single-center retrospective cohort study included 92 patients with systemic lupus erythematosus treated with belimumab. We analyzed the changes in flare free rate/lupus low disease activity state (LLDAS) attainment rate/glucocorticoid dosage/Systemic Lupus International Collaborating Clinics and American College of Rheumatology damage index (SDI) score/drug retention rate after treatment initiation. Results Fifty-two weeks after initiating belimumab, the flare rate decreased from 82.6% to 14.1% (p < .01). Until week 52 and 1000 days after initiating belimumab treatment, > 70% and ∼90% of the patients attained lupus low disease activity state, respectively. Belimumab treatment significantly reduced glucocorticoid demand (initiation day, 8.88 (6.00–15.00) mg/d; week 52, 5.00 (2.00–7.00) mg/d; final day of the study period, 3.00 (0.46–6.06) mg/d, initiation day vs. week 52: p < . 01, initiation day vs. final day: p < . 01); at the end of the study period, 68.5% of patients required ≤5 mg/d prednisolone, and 22.8% discontinued glucocorticoids. Most patients were SDI progression-free (week 52, ∼95%; day 1000, ∼90%), and belimumab showed a high drug retention rate (week 52, 90%; day 1000 > 80%). Conclusion Most patients experienced lupus low disease activity state, reduced flare rate and glucocorticoid demand, and a stable SDI trend after belimumab treatment initiation. Given its efficacy and retention rate, belimumab treatment may serve as a fundamental strategy in disease modification.
Sociodemographic differences in dietary trends among Iranian adults: findings from the 2005–2016 Iran-WHO STEPS survey

Abstract Objective: To examine trends in the intake of key food groups among Iranian adults between 2005 and 2016, overall, and according to sociodemographic characteristics. Design: Repeat cross-sectional data from the Iran-STEPwise approach to risk factor surveillance (Iran-WHO STEPS) 2005–2016 were analysed. Regression analyses were used to evaluate trends in the frequency of fruits, vegetables and fish intake and type of oil used over time. Interactions by sex, age and area of residence were examined. Setting: Iran. Participants: 225 221 Iranian adults. Results: The frequency of vegetables (β: −0·03; 95 % CI (−0·06, −0·00); P-trend = 0·030) and fish (β: −0·09; 95 % CI (−0·10, −0·08); P-trend < 0·001) intake and use of solid fat (OR: 0·70; 95 % CI (0·70, 0·72); P-trend < 0·001) declined, whilst the frequency of fruit intake (β-Coeff: 0·03, 95 % CI (0·01, 0·05); P-trend = 0·014) and liquid oil use (OR: 1·40; 95 % CI (1·3, 1·4); P-trend<0·001) rose. Rising trends in fruit intake were larger in mid-aged (40–60 years) and older (>60 years) adults (P-interaction < 0·001), whilst declines in vegetable (P-interaction < 0·001) and fish intake (P-interaction = 0·001) were larger in older adults. The declining use of solid fat was strongest in middle-aged and older adults (P-interaction = 0·035), while the increasing use of liquid oil was strongest in rural areas (P-interaction = 0·011). Conclusions: During the nutrition transition, liquid oil use and the frequency of fruit intake rose, while the frequency of vegetables and fish intake declined. Nonetheless, the fatty acid composition and cooking methods are important considerations. The changes observed are concerning from a public health perspective and demonstrate the need for interventions and possible targets for tailored strategies.
Transcriptome analysis reveals molecular signature and cell-type difference of Homo sapiens endothelial-to-mesenchymal transition

Abstract Endothelial-to-mesenchymal transition (EndoMT), a specific form of epithelial-to-mesenchymal transition, drives a growing number of human (Homo sapiens) pathological conditions. This emerging knowledge opens a path to discovering novel therapeutic targets for many EndoMT-associated disorders. Here, we constructed an atlas of the endothelial-cell transcriptome and demonstrated EndoMT-induced global changes in transcriptional gene expression. Our gene ontology analyses showed that EndoMT could be a specific checkpoint for leukocyte chemotaxis, adhesion, and transendothelial migration. We also identified distinct gene expression signatures underlying EndoMT across arterial, venous, and microvascular endothelial cells. We performed protein–protein interaction network analyses, identifying a class of highly connected hub genes in endothelial cells from different vascular beds. Moreover, we found that the short-chain fatty acid acetate strongly inhibits the transcriptional program of EndoMT in endothelial cells from different vascular beds across tissues. Our results reveal the molecular signature and cell-type difference of EndoMT across distinct tissue- and vascular-bed-specific endothelial cells, providing a powerful discovery tool and resource value. These results suggest that therapeutically manipulating the endothelial transcriptome could treat an increasing number of EndoMT-associated pathological conditions.
The sequence stratigraphy of Mesozoic successions in the Levant margin, southwestern Israel: A model for the evolution of southern Tethys margins

The Levant margin, in the subsurface of the eastern Mediterranean area, formed during the early Mesozoic following rifting and subsequent opening of the southern Tethys Ocean. This work describes the stratigraphic evolution of the shelf edge and slope for this margin in southwestern Israel and in the adjacent Mediterranean Sea. The study is based on the interpretation of 27 wells and 92 seismic reflection lines totaling 2000 km (1243 mi). Depositional sequences and sequence boundaries of the Jurassic and the Cretaceous age inferred from seismic reflection terminations, wireline-log stacking patterns, lithofacies, and biostratigraphic data. Six low-order and 22 high-order depositional cycles were identified. Their stratigraphic architecture reflects shifts of depocenters from the basin to its margin, controlled by eustasy and regional subsidence. Aggrading and backstepping of carbonate platforms in the Levant shelf is associated with relative rises in sea level. Progradation of siliciclastic and carbonate slopes toward the basin is related to relative drops in sea level. The stratigraphic framework of the Levant margin presented here is in accordance with recently published Mesozoic sequence stratigraphy of the Arabian platform, therefore, it may be used as a working model for reconstructing other rifted Tethyan margins in the region. This study further emphasizes the reservoir potential of Jurassic and Cretaceous deep-water lowstand wedges offshore Israel, where extensive exploration efforts are currently occurring.
Moderate-intensity aerobic exercise training as an adjunct to trauma-focused psychotherapy in traumatized refugees and asylum seekers: study protocol of a randomized controlled trial

ABSTRACT Background: Refugees with exposure to multiple traumatic events are at high risk for developing posttraumatic stress disorder (PTSD) and depression. Narrative exposure therapy (NET) is an effective treatment for the core symptoms of PTSD, but it does not reliably reduce depressive symptoms. Endurance exercise on the other hand was consistently found to be effective in treating depression making it a promising adjunct to NET. Up to date, no studies exist investigating the combination of NET and endurance exercise in a sample of refugees with PTSD and comorbid depression. Objectives: In the proposed randomized controlled trial, we aim to investigate whether a combination of NET and moderate-intensity aerobic exercise training (MAET) enhances treatment outcome for refugees with PTSD and comorbid depressive symptoms. We expect a greater improvement in psychopathology in participants who receive the combined treatment. Methods and analysis: 68 refugees and asylum seekers with PTSD and clinically relevant depressive symptoms will be recruited in the proposed study. Participants will be randomly assigned to receive either NET only (NET-group) or NET plus MAET (NET+-group). All participants will receive 10 NET sessions. Participants in the NET+-group will additionally take part in MAET. Primary (PTSD, depression) and secondary (general mental distress, agoraphobia and somatoform complaints, sleep quality) outcome measures will be assessed before treatment, after treatment, and at six-month follow-up. The hypotheses will be tested with multiple 2 × 3 mixed ANOVA's. Trial registration: German Clinical Trials Register identifier: DRKS00022145. HIGHLIGHTS Refugees are at particularly high risk of developing posttraumatic stress disorder and comorbid depressive symptoms due to exposure to multiple man-made traumatic events. Narrative exposure therapy reliably reduces symptoms of posttraumatic stress disorder, but many patients retain their clinical diagnosis, untreated comorbid depressive symptoms may interfere with treatment response. The randomized controlled trial aims to investigate whether combining narrative exposure therapy with moderate-intensity aerobic exercise training enhances treatment outcomes for refugees with posttraumatic stress disorder and comorbid depressive symptoms, compared to narrative exposure therapy as a stand-alone treatment.