Miracle-dz/UniFAR-FTUs huggingface dataset:
Superconductivity of Pb Ultrathin Film on Ge(111) Surface

We have performed structure analysis and electrical conductivity measurements of Pb ultrathin films of different thicknesses grown on Ge (111) at low temperature by using electron diffraction, scanning tunneling microscopy, and in-situ four-point probe method in ultrahigh vacuum. Three samples with different deposition amounts of Pb corresponding to 1, 3 and 10 monolayer (ML) were revealed to have different structures. The 1 ML-Pb sample, having a wetting layer and tiny clusters on it, did not show superconductivity. The 10-ML-Pb sample, consisted of continuous Pb (111) thin film structure, showed thin-film superconductivity around 6 K. The 3-ML-Pb sample, consisted of the wetting layer with unconnected Pb (111) islands on it, also showed superconductivity around 4 K. This superconductivity is thought to be induced in the wetting layer by proximity effect from superconducting Pb (111) islands. Thus, it is important to study the detailed growth structures for understanding atomic-layer superconductivity.
Smoking tobacco is associated with renal hyperfiltration

Abstract Tobacco consumption is a renal risk factor, but the effects on the estimated glomerular filtration rate (eGFR) remain unclear. We aimed to evaluate the possible impact of using tobacco products (smoking and snus) on eGFR based on creatinine or cystatin C. We used a first cohort with 949 participants and a second cohort with 995 participants; none had pre-existing renal disease. All subjects donated a blood sample and completed a questionnaire, including questions about tobacco use. To assess the effect on eGFR, hierarchical multiple linear regression models were used. Active smoking associated independently with a higher eGFRcreatinine in all subjects (p < 0.001; β = 0.11). Further analyses stratified for sex, showed similar findings for men (p < 0.001; β = 0.14) and for women (p = 0.026; β = 0.10). eGFRcystatin C was significantly associated with active smoking in all subjects (p = 0.040; β = −0.05), but no association was seen after stratification for sex. Snus did not associate with eGFR. In conclusion, smoking associated significantly with a higher eGFRcreatinine. The mechanism may be renal hyperfiltration of smaller molecules such as creatinine. This is probably caused by substances from smoked tobacco other than nicotine, as no effect was seen for snus.
Computed Tomography Perfusion–Based Prediction of Core Infarct and Tissue at Risk: Can Artificial Intelligence Help Reduce Radiation Exposure?

Supplemental Digital Content is available in the text. Background and Purpose: We explored the feasibility of automated, arterial input function independent, vendor neutral prediction of core infarct, and penumbral tissue using complete and partial computed tomographic perfusion data sets through neural networks. Methods: Using retrospective computed tomographic perfusion data from 57 patients, split as training/validation (60%/40%), we developed and validated separate 2-dimensional U-net models for cerebral blood flow (CBF) and time to maximum (Tmax) maps calculation to predict core infarct and tissue at risk, respectively. Once trained, the full sets of 28 input images were sequentially reduced to equitemporal 14, 10, and 7 time points. The averaged structural similarity index measure between the model-derived images and ground truth perfusion maps was compared. Volumes for core infarct and Tmax were compared using the Pearson correlation coefficient. Results: Both CBF and Tmax maps derived using 28 and 14 time points had similar structural similarity index measure (0.80–0.81; P>0.05) when compared with ground truth images. The Pearson correlation for the CBF and Tmax volumes derived from the model using 28-tp with ground truth volumes derived from the RAPID software was 0.69 for CBF and 0.74 for Tmax. The predicted maps were fully concordant in terms of laterality to the commercial perfusion maps. The mean Dice scores were 0.54 for the core infarct and 0.63 for the hypoperfusion maps. ConclusionS: Artificial intelligence model-derived volumes show good correlation with RAPID-derived volumes for CBF and Tmax. Within the constraints of a small sample size, the perfusion map quality is similar when using 14-tp instead of 28-tp. Our findings provide proof of concept that vendor neutral artificial intelligence models for computed tomographic perfusion processing using complete or partial image data sets appear feasible. The model accuracy could be further optimized using larger data sets.
High endothelial venule is a surrogate biomarker for T-cell inflamed tumor microenvironment and prognosis in gastric cancer

Background High endothelial venule (HEV) is a specialized vasculature for lymphocyte trafficking. While HEVs are frequently observed within gastric cancer (GC), the vascular–immune interaction between HEV and tumor-infiltrating lymphocytes (TILs) has not been well elucidated. In this study, we aimed to unveil the potential value of HEVs as a surrogate marker for T-cell inflamed immune microenvironment in GC using a large number of prospectively collected surgical specimens of GC. Methods We included 460 patients with GC who underwent surgical resection. Nanostring PanCancer immune profiling was performed to evaluate the immunological phenotype of GCs. HEV density and three distinct patterns of TILs (Crohn-like lymphoid reaction, peritumoral lymphoid reaction, and intratumoral lymphoid reaction) were analyzed for their relationship and evaluated as prognostic factors for relapse-free survival (RFS) and overall survival (OS). Results HEV-high GC revealed increased infiltration by immune cell subsets, including dendritic cells, CD8+ cytotoxic T cells, and CD4+ helper T cells. In addition, HEV-high GC demonstrated increased immune-modulating chemokines, type I or II interferon pathway, and immune checkpoints, all of which indicate the inflamed tumor microenvironment (TME). All three distinct patterns of TILs were associated with HEV density. In survival analysis, patients with HEV-high GC displayed significantly longer RFS and OS than those with HEV-low GC (p<0.001 for RFS, p<0.001 for OS). Multivariate analysis demonstrated that HEV was the most significant immunological prognostic factor for RFS (patients with high HEV compared with those with low HEV; HR 0.412, 95% CI 0.241 to 0.705, p=0.001) and OS (HR 0.547, 95% CI 0.329 to 0.909, p=0.02) after adjustment for age, stage, and TIL. Conclusion HEV is the most significant immunological prognosticator for RFS and OS in resected GC, indicating inflamed TME.
Simultaneous Evaluation of Membrane Permeability and UDP-Glucuronosyltransferase–Mediated Metabolism of Food-Derived Compounds Using Human Induced Pluripotent Stem Cell–Derived Small Intestinal Epithelial Cells

Pharmacokinetic prediction after oral ingestion is important for quantitative risk assessment of food-derived compounds. To evaluate the utility of human intestinal absorption prediction, we compared the membrane permeability and metabolic activities of human induced pluripotent stem cell–derived small intestinal epithelial cells (hiPSC-SIECs) with Caco-2 cells or human primary enterocytes (hPECs). We found that membrane permeability in hiPSC-SIECs had better predictivity than that in Caco-2 cells against 21 drugs with known human intestinal availability (r = 0.830 and 0.401, respectively). Membrane permeability in hiPSC-SIECs was only 0.019–0.25-fold as compared with that in Caco-2 cells for 7 in 15 food-derived compounds, primarily those that were reported to undergo glucuronidation metabolism. The metabolic rates of the glucuronide conjugate were similar or higher in hiPSC-SIECs as compared with hPECs but lower in Caco-2 cells. Expression levels of UDP-glucuronosyltransferase (UGT) isoform mRNA in hiPSC-SIECs were similar or higher as compared with hPECs. Therefore, hiPSC-SIECs could be a useful tool for predicting human intestinal absorption to simultaneously evaluate membrane permeability and UGT-mediated metabolism. SIGNIFICANCE STATEMENT Gastrointestinal absorption is an important step for predicting the internal exposure of food-derived compounds. This research revealed that human induced pluripotent stem cell–derived small intestinal cells (hiPSC-SIECs) had better predictivity of intestinal availability than Caco-2 cells; furthermore, the metabolic rates of UDP-glucuronosyltransferase (UGT) substrates of hiPSC-SIECs were closer to those of human primary enterocytes than those of Caco-2 cells. Therefore, hiPSC-SIECs could be a useful tool for predicting human intestinal absorption to simultaneously evaluate membrane permeability and UGT-mediated metabolism.
Small animal imaging presents an opportunity for improving translational research in biological psychiatry

Recent efforts in biological psychiatry have made a significant push toward examining both psychopathology and brain circuitry on a continuum across the spectrum of healthy individuals to those suffering from chronic and unremitting neuropsychiatric disorders.1 Neuroimaging methods have provided a critical tool through which to examine this continuum,2,3 given their noninvasive, repeatable nature. Additionally, they provide a scaffold through which one can relate sources of neurobiological heterogeneity (in the form of brain anatomy and function) to clinical and behavioural heterogeneity.4–6 In particular, magnetic resonance imaging (MRI) methods have been important in this regard, given the public availability of data and the multiple analysis streams that leverage different tissue properties to make inferences on brain topology and circuitry.7,8 Arguably, this sustained strategy contributed to recent significant advances in using knowledge of brain circuitry to target novel brain stimulation approaches as treatments for neuropsychiatric disorders9,10 and for improving our understanding of the mechanism of action of pharmacological agents (like ketamine) being repurposed for use in different clinical contexts.11 In aggregate, these developments are highly suggestive of how significant gains in novel therapeutics can be obtained using reliable investigations of well-characterized brain circuits. Despite these important advancements, there is still much work to do in understanding how neuropsychiatric disorders emerge over time. Human neuroimaging experiments, MRI in particular, lack the important ability to achieve detailed mechanistic insights that involve cellularor molecular-level information. There are notable exceptions, such as the use of positron emission tomography or magnetic resonance spectroscopy (and related techniques), for obtaining data on specific molecular phenotypes.12,13 Alternatively, one can relate neural phenotypes14–16 to gene expression data from public resources like the Allen Human Brain Atlas;17 however, these relationships are generally derived neuroinformatically and preclude the investigation of cellular and molecular phenotypes. There are limited means to perform detailed investigations across architectural scales (molecular, cellular, structural and functional connectivity, and morphology) in humans as one could perform using animal models of the central nervous system disorders. To this end, small animal imaging may provide meaningful opportunities in the context of biological psychiatry for bridging between macroand microanatomic scales of brain circuitry. In this editorial, we describe both the utility of MRI research (with an emphasis on the use of rodent models) for gaining mechanistic insight into neuropsychiatric illness and how dimensional approaches that have provided important advances in the clinical/ neuroimaging literature can be translated into experi mental design.
Preoperative nutritional state is associated with mid- and long-term mortality after cardiac surgery.

BACKGROUND The frailty score has been developed to determine physiological functioning capacity. The aim of our research was to explore the relationship between frailty factors and mortality in cardiac surgery patients. METHODS Our research is an observational, single-center, prospective cohort study (registered on ClinicalTrials.gov: NCT02224222), and we studied 69 patients who underwent elective cardiac surgery between 2014 and 2017. Thirty days before the surgery, they completed a questionnaire that contained questions related to social support, self-reported life quality-happiness, cognitive functions, anxiety and depression. Demographic, anthropometric and medical data were widely collected. The Geriatric Nutritional Risk Index (GNRI) and the Comprehensive Geriatric Assessment (CGA)-based frailty index were calculated as a sum and the domains, respectively. Cox regression and the Kaplan-Meier tests were applied to analyze survival and relative risk. The primary outcome was mid-term mortality. RESULTS The patients' mean age was 65.43 years [standard deviation (SD): 9.81 years]. The median followup was 1,656 days of survival [interquartile range (IQR), 1,336-2,081 years], during this period 14 patients died. The median of EuroSCORE II was 1.56 (1.00-2.58) points. The median preoperative albumin level was 32.80 g/L (IQR, 29.9-35.8 g/L). Major adverse cardiovascular and cerebral events (MACCEs) occurred 7 times during follow-up. The nutrition score of the CGA was significantly associated with worse long-term survival [score; hazard ratio (HR): 5.35; 95% CI: 1.10-25.91, P=0.037]. After adjustment for EuroSCORE II and postoperative complications the noncardiovascular CGA score was associated with overall mortality [adjusted hazard ratio (AHR): 1.44, 95% CI: 1.02-2.04, P=0.036]. In the multivariable Cox regression, GNRI <91 showed an increased risk for mortality (AHR: 4.76, 95% CI: 1.52-14.92, P=0.007). CONCLUSIONS The CGA-based noncardiovascular score and nutritional status should be assessed before cardiac surgery prehabilitation and may help decrease long-term mortality.
Opponensplasty using the extensor indicis proprius tendon for severe carpal tunnel syndrome in 40 patients

The aim of this study was to assess the clinical results after extensor indicis proprius opponensplasty in patients with carpal tunnel syndrome and severe thenar muscle atrophy. Forty patients who underwent this procedure during open carpal tunnel releases. The mean follow-up period was 17 months (range 10 to 36). Kapandji scores significantly improved from 5.5 before surgery to 9.6 at final follow-up. Thumb pronation angle also significantly improved from 111° before surgery to 149°. Side and pulp pinch strength significantly improved postoperatively, as well as DASH scores at final follow-up. In conclusion, the extensor indicis proprius tendon transfer technique represents a reliable opponensplasty procedure to achieve consistent results in patients with severe carpal tunnel syndrome. Level of evidence: IV
Clinical progression of COVID-19 coinfection in people living with the human immunodeficiency virus: scoping review.

OBJECTIVES to map the production of scientific knowledge on the clinical progression of COVID-19 coinfection in people living with the human immunodeficiency virus (HIV). METHODS scoping review, with search strategies in MEDLINE, Scopus, Embase, Web of Science, and LILACS. Dual independent data extraction and analysis of the material with similarity compilation and narrative synthesis. RESULTS sample consisted of 35 articles. Fever, cough, and dyspnea were the most prevalent signs/symptoms. Recurrent complications involved desaturation/worsening of oxygen desaturation and pneumonia. No standard pharmacological treatment was identified, and the main interventions involved the provision of supplemental oxygen and mechanical ventilation. The studies recommended preventive, care, and pharmacological practices. CONCLUSIONS the clinical manifestations, complications, and treatments/assistance care for people coinfected with SARS CoV-2/HIV are similar to those of the general population. Coinfection, overall, does not infer a worse prognosis.
Inferior outcomes with R-CEOP for patients with diffuse large B-cell lymphoma and cardiovascular comorbidities

Abstract Anthracycline-based chemoimmunotherapy with R-CHOP is the standard treatment for diffuse large B-cell lymphoma (DLBCL) but is associated with increased risks of cardiotoxicity. The alternative regimen R-CEOP substitutes etoposide for doxorubicin and is commonly administered to DLBCL patients with cardiovascular comorbidities, although there is limited evidence supporting its use. This multicenter real-world study included 138 consecutive patients with newly-diagnosed DLBCL treated with R-CEOP and 414 patients treated with R-CHOP matched 1:3 for age and International Prognostic Index. With median follow-up time 4.6 years, R-CEOP was associated with significantly inferior 4-year progression-free survival (32 vs. 52%, p < 0.0001), overall survival (39 vs. 59%, p < 0.0001), and disease-specific survival (48 vs. 69%, p < 0.0001) compared to R-CHOP. R-CHOP should remain the preferred regimen for most patients with DLBCL. While R-CEOP may be a reasonable choice for patients strictly ineligible for anthracyclines, the inferior outcomes of this regimen suggest that this high-risk population requires novel therapeutic approaches.
Association between Duration of Dialysis and Helicobacter Pylori Infection in Dialysis Patients at the University Clinical Hospital Mostar.

INTRODUCTION Association of Helicobacter pylori (HP) infection with the length of dialysis in dialysis patients is contradictory. This study was conducted in order to determine the association between the duration of dialysis and the HP infection status in the dialysis patients. Furthemore, biochemical parameters were monitored in two subject groups that were included in this study. SUBJECTS AND METHODS The study included 51 patients on chronic hemodialysis program who had gastrointestinal symptoms. The subjects were divided in two groups per the length of dialysis treatment. In this study we analyzed age, gender, the time period since the onset of the chronic hemodialysis program, body mass index, biochemical parameters, and whether the patients have arterial hypertension and/or diabetes. The presence of HP antigen was determined in the stool samples with use of he UlcoGnost AG test plate. RESULTS The incidence of HP infection in hemodialysis patients, with some of the gastrointestinal symptoms, was 25.5%. Patients on hemodialysis for less than 24 months had lower incidence of HP infection than those on hemodialysis program for more than 24 months. HP positive and HP negative subjects were also compared by gender, age, biochemical parameters and body mass index. There was no statistical significant difference between the groups in any of those characteristics. When comparing the HP status of the subjects with the presence of arterial hypertension and diabetes, no statistically significant difference was found between the groups. CONCLUSION This study showed negative correlation between HP infection and the length of hemodialysis program. Analysis of age, gender, body mass index, biochemical parameters, presence of arterial hypertension and/or diabetes showed no statistically significant difference was found between the hemodialysis patients who were HP positive and those who were HP negative. Additional studies are needed to elucidate the correlation mechanism between the HP infection and the duration of dialysis, in order to examine how long the dialysis time period is the most susceptible to HP infection, and then to improve the prognosis of patients with renal disease.
Intrinsic brainstem circuits comprised of Chx10-expressing neurons contribute to reticulospinal output in mice

Glutamatergic reticulospinal neurons in the gigantocellular reticular nucleus (GRN) of the medullary reticular formation can function as command neurons, transmitting motor commands to spinal cord circuits to instruct movement. Recent advances in our understanding of this neuron-dense region have been facilitated by the discovery of expression of the transcriptional regulator, Chx10, in excitatory reticulospinal neurons. Here, we address the capacity of local circuitry in the GRN to contribute to reticulospinal output. We define two sub-populations of Chx10-expressing neurons in this region, based on distinct electrophysiological properties and somata size (small and large), and show that these populations correspond to local interneurons and reticulospinal neurons, respectively. Using focal release of caged glutamate combined with patch clamp recordings, we demonstrated that Chx10 neurons form microcircuits in which the Chx10 local interneurons project to and facilitate the firing of Chx10 reticulospinal neurons. We discuss the implications of these microcircuits in terms of movement selection.
Effectiveness of esophagogastroduodenoscopy in changing treatment outcome in refractory gastro-esophageal reflux disease

Abstract Background/aims The effectiveness of screening esophagogastroduodenoscopy (EGD) for refractory gastroesophageal reflux disease (GERD) symptoms alone has not been validated. Methods We performed an observational study of patients with refractory GERD who underwent EGD from 2013 to 2016 at a tertiary hospital. Among 928 patients with GERD, we excluded patients with other alarm features, other indications for EGD, history of gastroesophageal surgery, or EGD done for other diagnostic procedures, and identified 301 patients who underwent EGD solely for persistent reflux symptoms such as heartburn or regurgitation. Results Among 301 patients with refractory GERD, 81.4% of patients were taking PPIs. 49.8% of patients had completely normal EGD findings and 33.6% of patients had benign or incidental findings. Two patients (0.6%) had LA grade C or D esophagitis, and 16.3% of patients had irregular Z line or salmon-colored mucosa. 91.0% (122/134) who had a biopsy had normal or benign findings. 4.0% (12/301) of patients had biopsy-proven intestinal metaplasia which is similar to the previously known prevalence of intestinal metaplasia in patients without heartburn (5.6%) and none had dysplasia or malignancy. Male sex was associated with endoscopic intestinal metaplasia suspected lesions in multivariate analysis (OR: 1.96, 95% CI: 1.04–3.70, p = .036) but not biopsy-proven intestinal metaplasia. Elderly age, obesity, alcohol or cigarette consumption, PPI use, GERD duration >3–5 years did not predict endoscopically suspected or biopsy-proven intestinal metaplasia. Only 5% of patients had a pH-impedance study for refractory reflux symptoms. Conclusions Most patients who underwent EGD for refractory GERD symptoms alone did not have pathological findings requiring a change in management. Screening EGD for patients only with persistent reflux symptoms should not be routinely recommended.
Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016–2017

We reconstructed the 2016–2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic’s origin, spread, and evolutionary dynamics. Our study revealed that the epidemic was propelled by multiple introductions that spread across the island, intricate evolutionary patterns, and ≈10 months of cryptic transmission.