Miracle-dz/UniFAR-FTUs huggingface dataset:
Incidence of Vancomycin Resistant Phenotype of the Methicillin Resistant Staphylococcus aureus Isolated from a Tertiary Care Hospital in Lahore

Staphylococcus aureus (S. aureus)-associated infections are one of the major threats to public health. The aim of the present study was to determine the antibiotic resistance pattern as well as the genetic characterization of methicillin and vancomycin resistant S. aureus (VRSA) isolated from a tertiary care hospital in Lahore. The S. aureus isolates were isolated from different clinical samples, identified by biochemical testing, and subjected to antibiotic susceptibility testing via the disc diffusion method or broth microdilution method. The methicillin resistance gene (mecA) and vancomycin resistance gene (vanA) were amplified by the polymerase chain reaction. The S. aureus isolates showed high incidences of resistance against methicillin (76%) and moderate incidences of resistance to vancomycin (14%). Isolates were also resistant to several other drugs, such as cefoxitin (76%), ertapenem (83%), ampicillin (81%), tobramycin (78%), moxifloxacin (76%), and tetracycline (74%). An encouraging finding was that 98% of isolates were susceptible to tigecycline, indicating its possible role in the treatment of methicillin-resistant Staphylococcus aureus (MRSA) and VRSA, as well as the multi-drug resistant S. aureus. The mecA gene was detected in 33.3% of tested isolates (10/30), while the vanA gene was also detected in 30% (9/30) of the tested isolates. In conclusion, the frequent presence of methicillin and vancomycin resistance in S. aureus appraises the cautious use of these antibiotics in clinical practices. Furthermore, it is suggested that there should be continuous monitoring of tigecycline treatments in clinical setups in order to delay the development of resistance against it.
Therapy of Type 2 Diabetes.

Affiliations 1 German Diabetes Foundationg, Munich, Germany 2 Section Endocrinology and Diabetology, University Obesity Centre Hamburg, University Hospital HamburgEppendorf, Germany 3 University Hospital Carl Gustav Carus at the TU Dresden, Department of Metabolic Vascular Medicine, Dresden and German Center for Diabetes Research (DZD e. V.), Neuherberg, Germany 4 Medical Clinic IV, University Hospital Tübingen, Germany 5 Centre for Internal Medicine I, Marienhospital, Stuttgart, Germany 6 Medical Clinic I, Berufsgenossenschaftliches University Hospital Bergmannsheil, Bochum, Germany 7 Medical Clinic I, University Hospital, Aachen, Germany 8 Diabetes Center Bochum-Hattingen, St.-Josef-Hospital, Ruhr-University, Bochum, Germany 9 Diabetological Practice, Jena, Germany 10 Department of Internal Medicine Gastroenterology, Diabetology/Endocrinology and Nutritional Medicine, St. Josefkrankenhaus Heidelberg GmbH, Heidelberg, Germany Bibliography DOI https://doi.org/10.1055/a-1018-9106 Exp Clin Endocrinol Diabetes 2019; 127 (Suppl 1): S73–S92 © J. A. Barth Verlag in Georg Thieme Verlag KG Stuttgart · New York ISSN 0947-7349
Polarimetric SAR Time-Series for Identification of Winter Land Use

In the past decade, high spatial resolution Synthetic Aperture Radar (SAR) sensors have provided information that contributed significantly to cropland monitoring. However, the specific configurations of SAR sensors (e.g., band frequency, polarization mode) used to identify land-use types remains underexplored. This study investigates the contribution of C/L-Band frequency, dual/quad polarization and the density of image time-series to winter land-use identification in an agricultural area of approximately 130 km² located in northwestern France. First, SAR parameters were derived from RADARSAT-2, Sentinel-1 and Advanced Land Observing Satellite 2 (ALOS-2) time-series, and one quad-pol and six dual-pol datasets with different spatial resolutions and densities were calculated. Then, land use was classified using the Random Forest algorithm with each of these seven SAR datasets to determine the most suitable SAR configuration for identifying winter land-use. Results highlighted that (i) the C-Band (F1-score 0.70) outperformed the L-Band (F1-score 0.57), (ii) quad polarization (F1-score 0.69) outperformed dual polarization (F1-score 0.59) and (iii) a dense Sentinel-1 time-series (F1-score 0.70) outperformed RADARSAT-2 and ALOS-2 time-series (F1-score 0.69 and 0.29, respectively). In addition, Shannon Entropy and SPAN were the SAR parameters most important for discriminating winter land-use. Thus, the results of this study emphasize the interest of using Sentinel-1 time-series data for identifying winter land-use.
The response of hepatitis B virus genotype to interferon is associated with a mutation in the interferon-stimulated response element

Abstract Genetic variation and genotype of Hepatitis B virus (HBV) are related to the efficiency of interferon alpha (IFN-α)-based antiviral therapy. However, the correlation of variation in interferon-stimulated response element (ISRE) and HBV genotype response to IFN-α therapy remains elusive. Differences of ISRE between genotype B and C HBV were explored using the HBV sequences retrieved from GenBank, and further investigated by ISRE region cloning and sequencing from 60 clinical samples post-IFN-α therapy. Additionally, ISRE mutants were constructed and their relation to responsiveness of IFN-α was evaluated by real-time PCR and Southern blot analysis. ISRE pattern between genotype B and C were found based on both clinical sample sequencing and full-length sequence alignment. The primary difference is the fourth base within the ISRE region, with T and C for genotype B and C, respectively. HBV with genotype C-type ISRE had a higher replicative capability as compared to HBV with genotype B-type ISRE after IFN-α treatment in huh7 cells. Conclusion: Preference of ISRE between genotype B and C HBV are distinct. Single nucleotide difference (C to T) within the HBV ISRE region may link to the efficacy of IFN-α therapy to genotype B and C HBV. Therefore, this study provides a clue for the determination of IFN-α therapy response to HBV treatment.
Biphasic Calcium Phosphate Sphere Graft Combined with a Double-Layer Non-Crosslinked Collagen Membrane Technique for Ridge Preservation: A Randomized Controlled Animal Study

The purpose of this study was to compare the histologic and radiologic differences between single- and double-layer collagen membrane techniques in flapless ridge preservation. The mandibular fourth premolar and first molar of four beagle dogs were used in the experiment. Mesial roots of the teeth were extracted and root canal treatment was performed at the distal roots. Ridge preservation was performed at the extraction sites using synthetic bone graft material. A single layer (control group) or double layer (test group) of non-crosslinked collagen membrane was applied following bone graft application. Three months later, the animals were sacrificed and micro-computed tomography (micro-CT) and histomorphometric analyses were conducted. Nonparametric Mann–Whitney test was performed to compare between the control and test groups. The vertical difference between buccal and lingual crests of control and test groups was 1.28 ± 0.41 and 0.53 ± 0.37 mm, respectively (p = 0.026). The mineralized bone area in control and test groups was 31.48% ± 7.41% and 42.25% ± 9.73%, respectively (p = 0.041). Within the limit of this study, ridge preservation using the double-layer membrane technique showed a reduced buccal bone resorption and improved new-bone formation in the ridge compared to that using the single-layer membrane technique.
Effects of Body Condition Score Changes During Peripartum on the Postpartum Health and Production Performance of Primiparous Dairy Cows

Simple Summary This study systematically describes the effects of body condition score (BCS) changes in primiparous cows during the peripartum period on hormone indexes, health, and production. The BCS and its changes indirectly measure the degree of fat mobilization and is a good predictor of the risk of postpartum disease. In production practice, confounding the management of primiparous and multiparous cow risks neglecting the postpartum characteristics of primiparous cows. A prospective observational study observed that primiparous cows that have a lower BCS have higher non-esterified fatty acids (NEFA) and β-hydroxybutyrate (BHBA) concentrations and more dramatic hormonal changes. Prepartum BCS changes were inconsistent and small, while after calving, there was a drastic decline in the BCS, suggesting that even a slight drop in the prepartum BCS may be a warning of a postpartum risk for primiparous cows. It is suggested that operators attach importance to the primiparous cow prepartum BCS and keep it stable through prepartum management adjustments, since an ideal BCS at calving reduces the incidence of postpartum disease. Abstract This is a prospective observational study that evaluates the effects of body condition score (BCS) changes in primiparous Holstein cows during peripartum on their NEFA and BHBA concentrations, hormone levels, postpartum health, and production performance. The cows under study (n = 213) were assessed to determine their BCS (5-point scale; 0.25-point increment) once a week during the whole peripartum by the same researchers; backfat was used for corrections. Blood samples were collected 21 and 7 days before calving and 7, 21, and 35 days after calving, and were assayed for NEFA, BHBA, growth hormone (GH), insulin, leptin, and adiponectin concentrations. The incidence of disease and milk yield were recorded until 84 days after calving. Cows were classified according to their BCS changes during peripartum as follows: Those that gained BCS (G; ΔBCS ≥ 0.25), maintained BCS (M; ΔBCS = 0–0.25), or lost BCS (L; ΔBCS ≥ 0.5). The BCS at −21 days and at 7, 14, and 21 days were different (p < 0.01), but trended toward uniformity in all groups at calving. The L group had higher NEFA and BHBA concentrations and hormone levels (p < 0.01) than the M and G groups at 21 and 35 days after calving, and had a higher incidence of uterine and metabolic diseases; however, there were no differences in production performance between the various groups. In conclusion, a lower BCS in primiparous cows during peripartum influences the NEFA and BHBA concentrations, hormone levels, and occurrence of health problems postpartum. The postpartum effects of BCS changes appear prior to calving.
Metal–Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy

Incorporation of a metal center into halogen-bonded materials can efficiently fine-tune the strength of the halogen bonds and introduce new electronic functionalities. The metal atom can adopt two possible roles: serving as halogen acceptor or polarizing the halogen donor and acceptor groups. We investigated both scenarios for 23 metal–halogen dimers trans-M(Y2)(NC5H4X-3)2 with M = Pd(II), Pt(II); Y = F, Cl, Br; X = Cl, Br, I; and NC5H4X-3 = 3-halopyridine. As a new tool for the quantitative assessment of metal–halogen bonding, we introduced our local vibrational mode analysis, complemented by energy and electron density analyses and electrostatic potential studies at the density functional theory (DFT) and coupled-cluster single, double, and perturbative triple excitations (CCSD(T)) levels of theory. We could for the first time quantify the various attractive contacts and their contribution to the dimer stability and clarify the special role of halogen bonding in these systems. The largest contribution to the stability of the dimers is either due to halogen bonding or nonspecific interactions. Hydrogen bonding plays only a secondary role. The metal can only act as halogen acceptor when the monomer adopts a (quasi-)planar geometry. The best strategy to accomplish this is to substitute the halo-pyridine ring with a halo-diazole ring, which considerably strengthens halogen bonding. Our findings based on the local mode analysis provide a solid platform for fine-tuning of existing and for design of new metal–halogen-bonded materials.
FOVEAL SPARING INTERNAL LIMITING MEMBRANE PEELING FOR IDIOPATHIC MACULAR HOLES: EFFECTS ON ANATOMICAL RESTORATION OF THE FOVEA AND VISUAL FUNCTION.

PURPOSE Muller cells seem to be important in maintaining foveal morphology through connections between their foot processes and the internal limiting membrane (ILM). Internal limiting membrane peeling causes Muller cell trauma. We hypothesized that leaving a rim of unpeeled ILM around idiopathic macular holes undergoing vitrectomy surgery would improve postoperative foveal morphology and vision. METHODS Prospective pilot study of fovea-sparing ILM peeling in a consecutive cohort of patients with macular holes over a 12-month period. Spectral-domain optical coherence tomography and Early Treatment Diabetic Retinopathy Study letters best-corrected visual acuity were assessed preoperatively and postoperatively, and foveal morphology and metamorphopsia postoperatively. The foveal sparing group was compared with a second consecutive cohort who received standard ILM peeling (control group). RESULTS Thirty-four eyes of 34 patients were included in each group. Groups showed no significant preoperative differences. 34/34 holes were successfully closed with surgery in the foveal sparing group and 32/34 in the control group. The foveal sparing group showed better postoperative best-corrected visual acuity (67.7 vs. 63.8, P = 0.003) and best-corrected visual acuity improvement (25.1 vs. 20.2, P = 0.03). The foveal sparing group demonstrated thicker minimum foveal thickness (211 vs. 173 μm, P = 0.002) and less steep foveal depression (158 vs. 149, P = 0.002). CONCLUSION Preserving nonpeeled ILM around macular holes resulted in a high closure rate, improved foveal morphology, and better postoperative best-corrected visual acuity. An appropriately powered randomized controlled study is warranted.
Triheptanoin Supplementation Does not Affect Nutritional Status: A Case Report of Two Siblings With Adult Polyglucosan Body Disease

Abstract Objective: An anaplerotic diet with the odd-chain triglyceride (triheptanoin-C7TG) supplementation was tested as a therapy for Adult Polyglucosan Body Disease (APBD) and is currently being assessed for various metabolic disorders. The aim of this study was to determine any unknown long-term effect of C7TG supplementation on the nutritional status, body composition, resting energy expenditure and biochemical parameters of two siblings with APBD. Methods: Two adult siblings with APBD were treated over a 2-year period with a high fat, low carbohydrate diet, with C7TG oil representing about 30% of the daily caloric intake. We carried out a long-term longitudinal study to determine weight, height, waist circumference; total, intra and extra cellular water by bioimpedance; body fat, lean mass, and bone mineral density by DEXA; resting energy expenditure by indirect calorimeter; glucose and lipid profiles. Results: C7TG supplementation failed to prevent APBD progression, corroborating recent literature. However, long-term C7TG supplementation did not produce any appreciable changes in nutritional status, body composition, resting energy expenditure or biochemical parameters, and no evidence was found of potential adverse effects. Conclusions: Our data suggest that maintenance of C7TG over a 2-year period still leaves a good safety profile in terms of nutritional status, body composition, resting energy expenditure, and biochemical parameters. However further studies involving larger sample sizes, also other diseases, are needed for a deeper understanding of its long-term effects.
Median sternotomy versus minimally invasive thymectomy for early-stage thymoma

Abstract Background: The completeness of resection is an important prognostic factor for early resectable thymoma. Since its inception 2 decades ago, median sternotomy has been recognized as the gold standard method for the treatment of all types and stages of thyomas. Minimally invasive surgical techniques, including video-assisted and robot-assisted surgery, have been rapidly developed as an alternative to traditional open approach surgery. Compared with traditional open approach surgery, minimally invasive approach has better cosmetic effect, faster improvement of lung function, reduction of surgical trauma, length of stay, and complications. We believe that this is an appropriate time and there is a need for a systematic, comprehensive, and objective assessment of the 2 surgical modalities in order to provide reliable evidence for clinicians to determine the best treatment for patients with early resectable thymoma. Methods: Pubmed (Medline), Web of Science, Embase, Cochrane Central Register of Controlled Trials, and Google Scholar will be searched for relevant randomized controlled trials (RCTs), quasi-RCTs, and Hi-Q (high quality) prospective cohort trials published or unpublished in any language before March 1, 2020. Subgroup analysis will be performed in tumor pathological stage and ethnicity. PROSPERO registration number: CRD42019133724. Results: The results of this study will be published in a peer-reviewed journal. Conclusion: This study will be the first to assess the efficacy and safety of median sternotomy recognized as the gold standard method for the treatment of all types and stages of thyomas and minimally invasive thymectomy for patients with early-stage thymoma. This study will assess whether minimally invasive thoracoscopic and robotic assisted thymectomy can be used as an alternative to traditional median sternotomy for patients with early resectable thymoma and provide high-quality and reliable evidence for clinicians’ decision-making.
A Human Lung Challenge Model to Evaluate the Safety and Immunogenicity of PPD and Live BCG.

BACKGROUND A human model to better understand tuberculosis immunopathogenesis and facilitate vaccine development is urgently needed. We evaluated the feasibility, safety, and immunogenicity of live Bacille-Calmette-Guerin (BCG) in a lung-orientated controlled human infection model. METHODS We recruited 106 healthy South African participants with varying degrees of tuberculosis susceptibility. Live BCG, sterile purified-protein-derivative (PPD), and saline were bronchoscopically instilled into separate lung segments (n=65). A control group (n=34) underwent a single bronchoscopy without challenge. The primary outcome was safety. Cellular and antibody immune signatures were identified in broncho-alveolar lavage fluid before, and three days after challenge using flow cytometry, ELISA, RNA sequencing and mass spectrometry. FINDINGS The frequency of adverse events was low (9.4%; n=10), similar in the challenge versus control groups (p=0.8), and were all mild and managed conservatively in an outpatient setting. The optimal PPD and BCG dose was 0.5 Tuberculin units, and 104 colony-forming units (CFU), respectively, based on changes in BAL cellular profiles (p=0.02) and antibody responses (p=0.01) at incremental doses pre- versus post-challenge. At 104, versus 103 CFU of BCG, there was a significant increase in number differentially expressed genes (367 versus 3; p<0.001) and dysregulated proteins (64 versus 0; p<0.001). Immune responses were highly setting-specific (in-vitro versus in-vivo), compartment-specific (BAL versus blood), and were localised to the challenged lung segments. CONCLUSION A lung-orientated mycobacterial controlled human infection model using live BCG and PPD is feasible and safe. These data inform the study of TB immunopathogenesis and strategies for evaluation and development of TB vaccine candidates.
Can amyloid PET differentiate “pure” LBD from AD with or without LBD copathology?

Neuropathologic studies have demonstrated that diagnoses of “pure” Alzheimer disease (AD) and “pure” Lewy body dementia (LBD) are not frequent, and AD pathology is often observed in non-AD dementias.1,2 The interpretation of biomarker measurements obtained during life in different forms of dementia is still a challenge. For example, interpretation of amyloid PET to define fibrillar β-amyloid (Aβ) in vivo in a sample that includes non-AD dementias can be complicated by uncertainty surrounding the contributions of diffuse vs neuritic plaques to the signal3 and whether other etiologies such as cerebral amyloid angiopathy may play a role.4,5
Galectin-8 binds to the Farnesylated C-terminus of K-Ras4B and Modifies Ras/ERK Signaling and Migration in Pancreatic and Lung Carcinoma Cells

K-Ras is the most prominent driver of oncogenesis and no effective K-Ras inhibitors have been established despite decades of intensive research. Identifying new K-Ras-binding proteins and their interaction domains offers the opportunity for defining new approaches in tackling oncogenic K-Ras. We have identified Galectin-8 as a novel, direct binding protein for K-Ras4B by mass spectrometry analyses and protein interaction studies. Galectin-8 is a tandem-repeat Galectin and it is widely expressed in lung and pancreatic carcinoma cells. siRNA-mediated depletion of Galectin-8 resulted in increased K-Ras4B content and ERK1/2 activity in lung and pancreatic carcinoma cells. Moreover, cell migration and cell proliferation were inhibited by the depletion of Galectin-8. The K-Ras4B–Galectin-8 interaction is indispensably associated with the farnesylation of K-Ras4B. The lysine-rich polybasic domain (PBD), a region that is unique for K-Ras4B as compared to H- and N-Ras, stabilizes the interaction and accounts for the specificity. Binding assays with the deletion mutants of Galectin-8, comprising either of the two carbohydrate recognition domains (CRD), revealed that K-Ras4B only interacts with the N-CRD, but not with the C-CRD. Structural modeling uncovers a potential binding pocket for the hydrophobic farnesyl chain of K-Ras4B and a cluster of negatively charged amino acids for interaction with the positively charged lysine residues in the N-CRD. Our results demonstrate that Galectin-8 is a new binding partner for K-Ras4B and it interacts via the N-CRD with the farnesylated PBD of K-Ras, thereby modulating the K-Ras effector pathways as well as cell proliferation and migration.
Neopterin is Associated with Disease Severity and Outcome in Patients with Non-Ischaemic Heart Failure

Inflammation and immune activation play an important role in the pathogenesis of cardiac remodelling in patients with heart failure. The aim of this study was to assess whether biomarkers of inflammation and immune activation are linked to disease severity and the prognosis of heart failure patients. In 149 patients (65.8% men, median age 49.7 years) with heart failure from nonischaemic cardiomyopathy, the biomarkers neopterin and C-reactive protein were tested at the time of diagnosis. Patients were followed-up for a median of 58 months. During follow-up, nineteen patients died, five had a heart transplantation, two needed a ventricular assistance device, and twenty-one patients had to be hospitalised because of heart failure decompensation. Neopterin concentrations correlated with N-terminal prohormone of brain natriuretic peptide (NT-proBNP) concentrations (rs = 0.399, p < 0.001) and rose with higher New York Heart Association (NYHA) class (I: 5.60 nmol/L, II: 6.90 nmol/L, III/IV: 7.80 nmol/L, p = 0.033). Higher neopterin levels were predictive for an adverse outcome (death or hospitalisation due to HF decompensation), independently of age and sex and of established predictors in heart failure such as NYHA class, NT-proBNP, estimated glomerular filtration rate (eGFR), and left ventricular ejection fraction (LV-EF) (HR 2.770; 95% CI 1.419–5.407; p = 0.003). Patients with a neopterin/eGFR ratio ≥ 0.133 (as a combined marker for immune activation and kidney function) had a more than eightfold increased risk of reaching an endpoint compared to patients with a neopterin/eGFR ratio ≤0.065 (HR 8.380; 95% CI 2.889–24.308; p < 0.001). Neopterin is associated with disease severity and is an independent predictor of prognosis in patients with heart failure.