Miracle-dz/UniFAR-FTUs huggingface dataset:
A simple ATAC-seq protocol for population epigenetics

We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
D-Limonene Alleviates Acute Kidney Injury Following Gentamicin Administration in Rats: Role of NF-κB Pathway, Mitochondrial Apoptosis, Oxidative Stress, and PCNA

Clinical application of gentamicin (GM) is well known to be associated with the development of acute kidney injury (AKI). This study was the first to investigate the possible protective effects of D-limonene (D-lim) on AKI following GM administration in rats. 32 rats arranged in four groups (n = 8): (1) the control group received saline intraperitoneally (0.5 ml/day) and orally (0.5 ml/day), (2) the D-lim group received D-lim (100 mg/kg) orally and saline (0.5 ml/day) intraperitoneally, (3) the GM group received GM (100 mg/kg/day) intraperitoneally and saline (0.5 ml/day) orally, and (4) the treated group received intraperitoneal GM (100 mg/kg) and oral D-lim (100 mg/kg). All treatments were performed daily for 12 consecutive days. Results revealed that D-lim ameliorated GM-induced AKI, oxidative stress, mitochondrial apoptosis, and inflammation. D-lim showed nephroprotective effects as reflected by the decrease in serum urea and creatinine and improvement of renal histopathological changes. D-lim alleviated GM-induced oxidative stress by increasing the activities of renal catalase, serum and renal glutathione peroxidase, and renal superoxide dismutase and decreasing renal malondialdehyde and serum nitric oxide levels. Intriguingly, D-lim suppressed mitochondrial apoptosis by considerably downregulating Bax and caspase-3 (Casp-3) mRNA and protein expressions and markedly enhancing Bcl2 mRNA and protein expressions. Furthermore, D-lim significantly decreases GM-induced inflammatory response through downregulation of NF-κB, IL-6, and TNF-α mRNA and/or protein expressions and decrease in renal myeloperoxidase activity. Finally, D-lim remarkably downregulated PCNA protein expression in the treated group compared with the GM group. In brief, this study showed that D-lim alleviated AKI following GM administration in rats, partially through its antioxidant, anti-inflammatory, and antiapoptotic activities as well as downregulation of PCNA expression.
The Impact of Inulin and a Novel Synbiotic (Yeast Saccharomyces cerevisiae Strain 1026 and Inulin) on the Development and Functional State of the Gastrointestinal Canal of Calves

Successful management of the dairy industry is closely related to rearing healthy calves. The proper development of the gastrointestinal canal is crucial to reach this goal. One of the strategies to promote this development is the addition of feed additives to the diet. This research aimed to determine the impact of prebiotic inulin and a new, not commercially available synbiotic (mix of prebiotic inulin and probiotic S. cerevisiae strain 1026) on the development of the gastrointestinal canal of calves by comparing the weight of the stomach, its relative ratio to body weight and evaluating pH, and histological changes in different parts of the gastrointestinal canal and assess whether or not the addition of inulin to the yeast S. cerevisiae improves the abovementioned parameters. We used prebiotic inulin (6 g) and a synbiotic (prebiotic inulin 6 g and probiotic Saccharomyces cerevisiae strain 1026, 5 g). The 56-day long research was conducted with fifteen crossbreed calves (32 ± 6 days old) organized in the control group (CoG), the prebiotic group (PreG), and the synbiotic group (SynG). We determined pH, morphological parameters of different parts of the digestive canal, and morphometric parameters of the stomach. The addition of prebiotic inulin to calves' diet causes the increase of pH in rumen, abomasum, and intestines but when inulin was added to S. cerevisiae, pH decreased and was even lower than in the control group. Prebiotic inulin and its synbiotic with yeast S. cerevisiae positively impact the development of almost all morphological structures of rumen saccus dorsalis, rumen saccus ventralis, and intestine; moreover, calves from the synbiotic group showed better results in virtually all parameters. However, both inulin and synbiotic did not affect the weight and relative weight of different parts of the stomach. Tested synbiotic has the potential to promote the development of the rumen and other parts of the digestive canal of calves.
Comparison of Effects of a Thrombin-Based Hemostatic Agent and Topical Tranexamic Acid on Blood Loss in Patients with Preexisting Thromboembolic Risk Undergoing a Minimally Invasive Total Knee Arthroplasty. A Prospective Randomized Controlled Trial

Background The efficacy of a thrombin-based hemostatic agent (Floseal®) on reducing postoperative blood loss after total knee arthroplasty (TKA) was still unclear. The aim of our study was to conduct a prospective randomized controlled study to compare the blood conservation effects of Floseal® and topical TXA in patients with preexisting thromboembolic risk undergoing primary minimally invasive TKA. Methods Our power analysis of this study was based upon the following description, to obtain a statistical power of 0.90 and an alpha error of 0.05, 30 patients were required in each group. Therefore, we enrolled a total of 103 patients with at least one of the risk factors for thromboembolism who underwent unilateral primary minimally invasive TKA, and the participants were randomly divided into the topical TXA group (n = 34), receiving intra-articular injection of 3 g of TXA in 100 mL saline after TKA, the topical Floseal® group (n = 34), receiving 10 mL of Floseal® intra-articularily during surgery, and the placebo group (n = 35), receiving an intra-articular saline injection only. The total blood loss (TBL) and hemoglobin (Hb) drop were compared among the 3 groups. Results The TXA group had a lower TBL of 645 mL (227 to 1090) in comparison with 1145 mL (535 to 1942) in the Floseal® group and 1103 mL (424 to 1711) in the placebo (p < 0.001, respectively). The TBL was similar between the Floseal® group and the placebo group (p = 0.819). No patients in any group had symptoms of venous thromboemblism. Conclusion Our prospective randomized controlled study showed that intra-articular application of TXA was superior to hemostatic matrix (Floseal®) in terms of blood conservation in patients with preexisting thromboembolic risk undergoing minimally invasive TKA. This trial is registered with Clinicaltrials.gov (NCT02865174) on 08/09/2016.
Validation of the German Version of the New Freezing of Gait Questionnaire for People with Parkinson‘s Disease

Freezing of gait (FOG) in Parkinson's disease (PD) is a highly disabling symptom which impacts quality of life. The New FOG Questionnaire (NFOG-Q) is the most commonly used tool worldwide to characterize FOG severity in PD. This study aims to provide a German translation of the NFOG-Q and to assess its validity in people with PD. The questionnaire was translated using forward-backward translation. Validity was tested in 57 PD patients with FOG via Cronbach's alpha for internal consistency and Spearman correlations with several clinical measures to quantify disease severity, mobility, fall risk, and cognitive state for convergent and divergent validity. The German version of the NFOG-Q shows good internal consistency (Cα = 0.84). Furthermore, the NFOG-Q score was significantly correlated with the MDS-UPDRS III, H&Y stage, Timed Up and Go test, and the subjective fear of falling (FES-I). The lack of correlation with cognition (MoCA) points towards good divergent validity. This study provides a German version of the NFOG-Q which proved to be valid for the assessment of FOG severity in individuals with PD.
Resource allocation decision-making in dementia care with and without budget constraints: a qualitative analysis

Introduction: Health systems in many different countries have increasingly been reorienting the delivery of dementia care to home and community care settings. This paper provides information on how health and social care professionals (HSCPs) in Ireland make decisions on resource allocation for people with dementia living at home and how resource constraints affect their decisions and choices. Methods: A balance of care approach was used to assess resource allocation across six dementia case types, from low to high needs. Workshops were held with 24 HSCPs from multiple disciplines. Participants allocated services in two scenarios: allocation with and without a budget constraint. Nominal group technique was used to structure discussions around resource allocation in both scenarios. Thematic analysis was applied to analyse the qualitative data using a general inductive approach. Results: The following themes influenced allocative deliberations: whose needs are being met; what needs are identified; decision making context; decision making process; and allocation outcomes. Participants were proficient in making decisions, using ‘decision rules’ or heuristics to help them make decisions under fixed budget rules and sticking to conventional provision when constraints were in place. Conclusions: Freedom from a budget constraint allowed HSCPs to consider a broader range of services and to take a more expansive view on what needs should be considered, with a particular emphasis on adopting a proactive, preventative approach to the allocation of resources. The effect of the budget constraint overall was to narrow all considerations, using heuristics to limit the type of needs addressed and the range of services and supports provided. The consequences were a largely reactive, less personalised system of care. The findings emphasise the need for an integrated and comprehensive assessment process that is more concerned with individualised responses rather than relying on existing models of care alone.
A preliminary comparative study of percutaneous CT-guided cryoablation with surgical resection for osteoid osteoma

Background The traditional treatment for osteoid osteoma is the nidus’ surgical resection, which was difficult to eradicate with more invasive and complications because of osteosclerosis surrounding the nidus. This study aimed to analyze the efficacy and safety of percutaneous CT-guided cryoablation of osteoid osteoma at different sites (especially refractory sites such as the spine). Methods Fifteen patients with osteoid osteoma who underwent cryoablation at our institution were analyzed retrospectively on their imaging data and clinical visual analog scale (VAS) pain scores before and after the procedure. Fifty-three patients underwent surgical resection during the period were also included in this study as a control group. Treatment efficacy was assessed primarily by comparing the differences in VAS scores at different time points in each group of patients by paired-sample t-test. Differences in length of hospital stay and complications between the two groups were also compared. Results The technical success rate was 100% in both the cryoablation and surgical resection group. Cryoablation had a significantly shorter hospitalization time than surgery (p = 0.001). Clinically, the post-operative VAS scores were all significantly improved compared to the pre-operative period, and the clinical cure was achieved in both groups. Surgical operations had more complications than cryoablation, although there was no significant difference. In the group of cryoablation, only one patient had mild numbness of the left lower extremity, which relieved itself; two patients had mild post-operative pain. No patients in the cryoablation group experienced recurrence during the follow-up period. In the surgery group, three of the patients experienced massive bleeding (>500 ml), and two underwent transfusion therapy. Only one patient in the surgical resection group experienced a recurrence at 29 months postoperatively and underwent a second resection. All patients had local scars on the skin after surgical resection. Conclusion Cryoablation is a minimally invasive, safe, and effective treatment strategy for osteoid osteoma, and is fully comparable to surgical resection.
Enteropathogenic Infections: Organoids Go Bacterial

Enteric infections represent a major health care challenge which is particularly prevalent in countries with restricted access to clean water and sanitation and lacking personal hygiene precautions, altogether facilitating fecal-oral transmission of a heterogeneous spectrum of enteropathogenic microorganisms. Among these, bacterial species are responsible for a considerable proportion of illnesses, hospitalizations, and fatal cases, all of which have been continuously contributing to ignite researchers' interest in further exploring their individual pathogenicity. Beyond the universally accepted animal models, intestinal organoids are increasingly valued for their ability to mimic key architectural and physiologic features of the native intestinal mucosa. As a consequence, they are regarded as the most versatile and naturalistic in vitro model of the gut, allowing monitoring of adherence, invasion, intracellular trafficking, and propagation as well as repurposing components of the host cell equipment. At the same time, infected intestinal organoids allow close characterization of the host epithelium's immune response to enteropathogens. In this review, (i) we provide a profound update on intestinal organoid-based tissue engineering, (ii) we report the latest pathophysiological findings defining the infected intestinal organoids, and (iii) we discuss the advantages and limitations of this in vitro model.
Balloon Valvuloplasty for Congenital Aortic Stenosis: Experience at a Tertiary Center in a Developing Country

Background Aortic valve stenosis accounts for 3–6% of congenital heart disease. Balloon aortic valvuloplasty (BAV) is the preferred therapeutic intervention in many centers. However, most of the reported data are from developed countries. Materials and Methods We performed a retrospective single-center study involving consecutive eligible neonates and infants with congenital aortic stenosis admitted for percutaneous BAV between January 2005 and January 2016 to our tertiary center. We evaluated the short- and mid-term outcomes associated with the use of BAV as a treatment for congenital aortic stenosis (CAS) at a tertiary center in a developing country. Similarly, we compared these outcomes to those reported in developed countries. Results During the study period, a total of thirty patients, newborns (n = 15) and infants/children (n = 15), underwent BAV. Left ventricular systolic dysfunction was present in 56% of the patients. Isolated AS was present in 19 patients (63%). Associated anomalies were present in 11 patients (37%): seven (21%) had coarctation of the aorta, two (6%) had restrictive ventricular septal defects, one had mild Ebstein anomaly, one had Shone's syndrome, and one had cleft mitral valve. BAV was not associated with perioperative or immediate postoperative mortality. Immediately following the valvuloplasty, a more than mild aortic regurgitation was noted only in two patients (7%). A none-to-mild aortic regurgitation was noted in the remaining 93%. One patient died three months after the procedure. At a mean follow-up of 7 years, twenty patients (69%) had more than mild aortic regurgitation, and four patients (13%) required surgical intervention. Kaplan–Meier freedom from aortic valve reintervention was 97% at 1 year and 87% at 10 years of follow-up. Conclusion Based on outcomes encountered at a tertiary center in a developing country, BAV is an effective and safe modality associated with low complication rates comparable to those reported in developed countries.
Use of Network Pharmacology to Investigate the Mechanism by Which Allicin Ameliorates Lipid Metabolism Disorder in HepG2 Cells

Allicin has been well documented to exhibit a wide spectrum of biological activities, especially lipid-lowering activity, as a promising candidate for the management of nonalcoholic fatty liver disease (NALFD). However, the mechanisms underlying the therapeutic effects of allicin require further investigation. It is tempting to think of combining network pharmacology and experimental validation to investigate the mechanism by which allicin ameliorates lipid metabolism disorder in HepG2 cells. We established a cell model of hepatic steatosis induced by PA to investigate the antisteatotic effects of allicin. The studies showed that allicin reduced PA-induced lipid accumulation using Nile red staining and TC and TG assays. Then, 219 potential targets of allicin were successfully predicted by PharmMapper. According to Reactome Pathway Analysis, 44 potential targets related to lipid metabolism were screened out. Molecular signaling cascades mediated by allicin included PPARA, PPARG, FABP4, and FABP6 by cytoHubba and qPCR analysis. Results revealed that allicin activated the gene expression of PPARA and FABP6 and suppressed the gene expression of FABP4 and PPARG. Thus, the present study united the methods of network pharmacology and experimental validation to investigate the protein targets of allicin on PA-induced lipid metabolism disorders to supply a reference for related application for the first time.
Real World First-Line Treatments and Outcomes of Nab-Paclitaxel Plus Gemcitabine, mFOLFIRINOX and GEMOX in Unresectable Pancreatic Cancer from a Chinese Single Institution

Background: There have not been any head-to-head prospective studies to compare the effects of different chemotherapy regimens as first-line treatments for unresectable pancreatic cancer (UPC). We aimed to compare the effectiveness of nab-paclitaxel plus gemcitabine, mFOLFIRINOX and gemcitabine plus oxaliplatin (GEMOX) as first-line treatments by using real-world data from Chinese patients. Methods: We retrospectively included patients with UPC treated with nab-paclitaxel plus gemcitabine, mFOLFIRINOX or GEMOX as a first-line treatment at Sun Yat-sen University Cancer Center. Overall survival (OS), progression-free survival (PFS), objective response rate (ORR) and disease control rate (DCR) were assessed. Results: A total of 117 patients were administered nab-paclitaxel plus gemcitabine (n = 62), mFOLFIRINOX (n = 30) or GEMOX (n = 25) as first-line chemotherapy. The median OS was 11.1, 10.1 and 10.2 months (p = 0.75) in the nab-paclitaxel plus gemcitabine, mFOLFIRINOX and GEMOX, respectively. The ORR was similar among the three groups (24%, 23% and 32%, p = 0.76) and the DCR was higher in the nab-paclitaxel-gemcitabine group (82%) than the other two groups (60% and 64%, p = 0.04). The most common adverse events of grade 3 or 4 were neutropenia (32%, 28% and 5%), peripheral neuropathy (13%, 16% and 0) and fatigue (9%, 16% and 5%). Febrile neutropenia occurred in 2%, 4% and 5% of the patients in the three groups. Conclusion: In the first line treatment of UPC, our results suggest that nab-paclitaxel plus gemcitabine was associated with a higher DCR than mFOLFIRINOX or GEMOX, while all groups demonstrated similar OS, PFS and ORR.
Natural Killer T Cells in Various Mouse Models of Hepatitis

Natural killer T (NKT) cells are a key component of innate immunity. Importantly, a growing body of evidence indicates that NKT cells play an integral role in various acute and chronic liver injuries. NKT cells participate in the progression of an injury through the secretion of cytokines, which promote neutrophil infiltration and enhance Fas ligand (FasL) and granzyme-mediated NKT cytotoxic activity. Therefore, examining the role of NKT cells in hepatic disease is critical for a comprehensive understanding of disease pathogenesis and may provide insight into novel approaches for treatment. For more than a century, mouse models that imitate the physiopathological conditions of human disease have served as a critical tool in biological and medical basic research, including studies of liver disease. Here, we review the role of NKT cells in various mouse models of hepatitis.
Determinants of Health Promotion Behaviors among Family Caregivers of Stroke Survivors

Purpose:To record the health promotion behaviors of family caregivers of stroke survivors, as well as potential determinants that could affect these behaviors. Methods: A cross-sectional study was carried out through home visits in the Attica region using the convenience sampling method. The studied population included 109 survivors who had suffered a stroke and experienced functional problems, and their 109 primary caregivers, who were family members, lived in the same house and were fully responsible for their care. The dependent variables were the caregivers’ health promotion behaviors, while the independent variables were the survivors and caregivers’ demographic characteristics, survivors’ functional capacity, depression, social support and changes in caregivers’ lives from caring. Results: Better health promotional behaviors were associated with the following: patient having advanced age and a high level of functionality, caregivers assessing their own state of health as “good”, greater social support, a higher educational level and a higher income level. In addition, more hours of patient care were associated with a less healthy lifestyle for caregivers. Conclusions: Promoting the health of family caregivers of stroke survivors is crucial for both survivors and caregivers. For this reason, it is of great importance to detect factors that affect the health promotion behaviors of caregivers in order to carry out appropriate interventions and improve their quality of life.
The prognostic value of seminal anti-sperm antibodies screening in men prepared for ICSI: a call to change the current antibody-directed viewpoint of sperm autoimmunity testing

Aims: We aimed to prospectively evaluate the prognostic value of seminal anti-sperm antibodies (ASA) screening in couples prepared for intracytoplasmic sperm injection (ICSI). Methods: A prospective comparative study was conducted, including 184 non-azoospermic infertile men scheduled for ICSI. For each patient, detection of ASA in seminal plasma using the ELISA technique was done and its relation to standard semen parameters and ICSI outcomes, including fertilization, embryo development, and pregnancy rates, was analyzed. Results: Sperm count, motility, and morphology were negatively affected by existence of seminal ASA (p = 0.012, 0.006, and 0.011, respectively). However, no statistically significant difference was detected between patients with positive and negative seminal ASA regarding the median values of fertilization (56.3% versus 66.7%, p = 0.091), percentage of couples with grade A embryo development (91.4% versus 89.9%, p = 0.520), and pregnancy rates (31.4% versus 32.2%, p = 0.98) after ICSI. Conclusion: ICSI seems able to overcome the problem of ASA in semen. The routine screening of ASA in men prepared for ICSI has no additional prognostic value and cannot be recommended for the time being, until more specific antigen-concerned testing can be developed.