Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Probiotic E. coli Nissle 1917 Supplementation on the Growth Performance, Immune Responses, Intestinal Morphology, and Gut Microbes of Campylobacter jejuni Infected Chickens

Campylobacter jejuni is the most common cause of bacterial foodborne gastroenteritis and holds significant public health importance. The continuing increase of antibiotic-resistant Campylobacter necessitates the development of antibiotic-alternative approaches to control infections in poultry and in humans. ABSTRACT Campylobacter jejuni is the most common cause of bacterial foodborne gastroenteritis and holds significant public health importance. The continuing increase of antibiotic-resistant Campylobacter necessitates the development of antibiotic-alternative approaches to control infections in poultry and in humans. Here, we assessed the ability of E. coli Nissle 1917 (EcN; free and chitosan-alginate microencapsulated) to reduce C. jejuni colonization in chickens and measured the effect of EcN on the immune responses, intestinal morphology, and gut microbes of chickens. Our results showed that the supplementation of 3-week-old chickens daily with free EcN in drinking water resulted in a 2.0 log reduction of C. jejuni colonization in the cecum, whereas supplementing EcN orally three times a week, either free or microencapsulated, resulted in 2.0 and 2.5 log reductions of C. jejuni colonization, respectively. Gavaged free and microencapsulated EcN did not have an impact on the evenness or the richness of the cecal microbiota, but it did increase the villous height (VH), crypt depth (CD), and VH:CD ratio in the jejunum and ileum of chickens. Further, the supplementation of EcN (all types) increased C. jejuni-specific and total IgA and IgY antibodies in chicken’s serum. Microencapsulated EcN induced the expression of several cytokines and chemokines (1.6 to 4.3-fold), which activate the Th1, Th2, and Th17 pathways. Overall, microencapsulated EcN displayed promising effects as a potential nonantibiotic strategy to control C. jejuni colonization in chickens. Future studies on testing microencapsulated EcN in the feed and water of chickens raised on built-up floor litter would facilitate the development of EcN for industrial applications to control Campylobacter infections in poultry.
A new attention-based 3D densely connected cross-stage-partial network for motor imagery classification in BCI

Objective. The challenge for motor imagery (MI) in brain-computer interface (BCI) systems is finding a reliable classification model that has high classification accuracy and excellent robustness. Currently, one of the main problems leading to degraded classification performance is the inaccuracy caused by nonstationarities and low signal-to-noise ratio in electroencephalogram (EEG) signals. Approach. This study proposes a novel attention-based 3D densely connected cross-stage-partial network (DCSPNet) model to achieve efficient EEG-based MI classification. This is an end-to-end classification model framework based on the convolutional neural network (CNN) architecture. In this framework, to fully utilize the complementary features in each dimension, the optimal features are extracted adaptively from the EEG signals through the spatial-spectral-temporal (SST) attention mechanism. The 3D DCSPNet is introduced to reduce the gradient loss by segmenting the extracted feature maps to strengthen the network learning capability. Additionally, the design of the densely connected structure increases the robustness of the network. Main results. The performance of the proposed method was evaluated using the BCI competition IV 2a and the high gamma dataset, achieving an average accuracy of 84.45% and 97.88%, respectively. Our method outperformed most state-of-the-art classification algorithms, demonstrating its effectiveness and strong generalization ability. Significance. The experimental results show that our method is promising for improving the performance of MI-BCI. As a general framework based on time-series classification, it can be applied to BCI-related fields.
Hematological and molecular analyses of the HbS allele among the Sudanese population

Objective The purpose of this study was to perform hematological and molecular analyses of the HbS allele of the hemoglobin subunit beta gene in the Sudanese population. Methods This was a descriptive cross-sectional study. Hematological parameters and fetal hemoglobin (HbF) levels were assessed in all participants. Data were gathered through the use of questionnaires and laboratory investigations. The βS-globin haplotypes, S allele distributions, and hematological parameters with HbF levels were investigated using PCR-restriction fragment length polymorphism, gel electrophoresis, and a Sysmex hematology analyzer, respectively. Results According to our findings, the Bantu (BA) haplotype was found in 10.8% of participants with homozygous uncontested haplotypes, followed by Benin (BA) and Sudan (SU), each in 9.8% of participants. This Sudanese group from Northern Kordofan lacked the Arab-Indian haplotype. Two heterozygous versions of undisputed haplotypes were found in 17.3% of participants: SU/BA in 10.8% and CA/BE in 6.5%. Conclusion As a result of sickle cell anemia, this investigation found changes in hematological parameters. In the Sudanese population, a new haplotype of the S gene was discovered.
Comparative zinc tolerance and phytoremediation potential of four biofuel plant species

Abstract Soil pollution has become a serious environmental problem worldwide due to rapid industrialization and urbanization. Zinc (Zn) contamination has raised concerns about potential effects on plants and human health. This study was conducted to assess the capability of four biofuel plants: Abelmoschus esculentus, Avena sativa, Guizotia abyssinica, and Glycine max to remediate and restore Zn contaminated soil. Selected plants were grown in soil exposed to different Zn treatments (50, 100, 200, 300, 400, 600, 800 and 1000 mg Zn kg−1) for 12 weeks. Soil without spike taken as control. Zn induced toxicity significantly (p < 0.05) reduced seed germination and inhibited plant growth and leaf chlorophyll content. The investigated plants can tolerate a soil content of 800 mg Zn kg−1 with the exception of A. sativa, which was most tolerant to high Zn concentrations (1000 mg Zn kg−1) for all growth criteria. Moreover, increasing Zn content in soil resulted in a significant (p < 0.05) increase in Zn accumulation in various tissues of the four biofuel plants. According to phytoremediation efficiency, the four biofuel plants studied were arranged as follows: A. sativa (5.05%) > A. esculentus (4.15%) > G. max (2.31%) > G. abyssinica (1.17%). This study concluded that all tested biofuel plants species, especially A. sativa exhibited high Zn concentrations in roots and shoots, high Zn uptake capability, high tolerance, and high biomass at 50–800 mg Zn kg−1 treatments. Consequently, these biofuel plants are excellent candidates for phytoremediation in Zn contaminated soils. Novelty statement Heavy metal contamination of soil poses a serious threat to the environment. Physical and chemical remediation methods are commonly used to remediate metal contaminated sites. It is not commercially viable, except that it is harmful and causes soil degradation. Alternatively, biological remediation techniques are cheap and environmentally friendly. Different plant species have been found to differ in their ability to accumulate metals under contaminated soil. Therefore, the present study provides a unique opportunity to study the metal accumulation potential of four biofuel plants (Abelmoschus esculentus, Avena sativa, Guizotia abyssinica and Glycine max) under zinc metal spiked soils. These plants are able to grow rapidly by developing a strong root system, high biomass production, and high tolerance to metal toxicity that helps them survive in contaminated soil environments. The investigated biofuel plant can be used to decontaminate contaminated sites and serves as a source of commercially valuable products that extract metals from biomass through combustion.
Risk factors and mortality associated with permanent pacemaker after surgical or transcatheter aortic valve replacement: Early versus late implantation

Inflation of transcatheter aortic valve replacement (TAVR) procedures compared to surgical aortic valve replacement (SAVR) has increased the number of patients requiring a postprocedure permanent pacemaker (PPM). We investigate the impact of PPM on mid‐term mortality comparing SAVR versus TAVR procedures and risk factors for early and late (>14 days) need of PPM.
Neuropsychiatric manifestations are associated with increased mortality in Indian patients with lupus: A single centre retrospective observational study

Objective To study the prevalence of different NPSLE manifestations in our cohort and to compare clinical and immunological features and outcomes including mortality of patients with NPSLE and SLE controls without NP involvement. Methods This was a retrospective study in a tertiary care referral centre. All patients of SLE seen in the last 10 years and fulfilling the SLICC criteria with neuropsychiatric manifestations as per the ACR definitions were included. Patients of SLE without NP involvement were sequentially assigned as controls in a ratio of 1:2. Results Of the 769 patients diagnosed with SLE from Jan 2011 to December 2020, 128 (16.6%) had NPSLE manifestations as per the ACR definitions. The commonest NPSLE manifestation was seizures (6.5%) followed by cerebrovascular accident (3.9%). NPSLE manifestation occurred at the first presentation of SLE in 99/128 (77.3%) patients and 58 (45.3%) patients had more than one NPSLE manifestation. Lupus anticoagulant and anticardiolipin antibody were tested in 120 patients and were positive in 16 (13.3%) and 12 (10%), respectively. No difference was found in anti-ribosomal p, lupus anticoagulant and anticardiolipin antibodies between the cases and controls. Twenty-one (16.4%) deaths occurred in patients with NPSLE (median follow-up of 40 months) as compared to 13 (5%) in controls (median follow-up of 32 months) (p = <0.001). The cumulative survival of patients with NPSLE was lower as compared to controls (p < 0.001). Relapse of NPSLE was seen in 11(8.6%) patients and was associated with mortality (p = 0.017). Conclusions Seizures and cerebrovascular accidents are the commonest NPSLE syndromes in our patients. The presence of NPSLE was associated with high mortality in Indian patients with lupus.
Metastasis of a basosquamous carcinoma arising in a nevus sebaceus

Nevus sebaceus (NS) is a congenital hamartoma of skin structures including the epidermis, sweat sebaceous glands, and hair follicles. It is known that secondary tumors can occur in NS. However, secondary metastatic malignancies are rare. Basosquamous carcinoma (BSC) is an aggressive type of basal cell carcinoma (BCC) characterized by squamous differentiation. Herein, we report a case of metastatic BSC that developed in a 73‐year‐old male with NS. The clinical presentation of this patient was that of an ulcerative nodule developing in a longstanding plaque‐like lesion consistent with NS. Histopathological examination revealed characteristic features of BCC with some areas of squamous differentiation in addition to the structure of a typical NS. Immunohistochemical expression of Ber‐EP4, AE1/AE3, and epithelial membrane antigen helped to make the diagnosis of BSC.
Two Decades’ Outcomes and Trends of Adrenalectomy for Benign Pathologies in Veterans

Background: Since the introduction of laparoscopic adrenalectomy (LA) in 1992, it has become the standard of care for most adrenal benign pathologies. This study compares the outcomes and trends of open (OA) versus LA in veterans for benign pathologies. Methods: Veterans Affairs Surgical Quality Improvement Program was queried for adrenalectomies performed for benign pathologies during the period 2000-2019. Data collection included demographics, comorbidities, operative details, and postoperative outcomes. Results: A total of 1683 patients were included (91.4% males, mean age 59.6, mean body mass index 31.2, and 87.2% with American Society of Anesthesiologists class≥III). Overall, the mean operative time (OT) was 3.2 hours, the majority performed by general surgeons (71.4%), and the mean length of stay (LOS) was 4.1 days. There were 12 (0.7%) 30-day mortalities, and 162 patients (8.8%) developed ≥1 complication. LA was performed in 70.9% (1306), with the conversion rate of 0.85% (10). When compared with OA, patients with the laparoscopic approach were functionally independent, shorter OT, less intraoperative blood transfusion, shorter LOS, and lower mortality and morbidity. Dependent functional status, congestive heart failure, American Society of Anesthesiologists class ≥III, and smoking were independent predictors of mortality, whereas intraoperative transfusions, chronic obstructive pulmonary disease, and dependent functional status were predictors of morbidity. Trend analysis showed an 8-fold increase in the use of LA. However, trend analysis for morbidity and mortality rates showed no significant change for both approaches. Conclusion: LA is being well adopted in the veterans affairs system with an 8-fold increase over 20 years, with lower morbidity and mortality compared with the open approach for benign adrenal pathologies.
Commensal Fungus Candida albicans Maintains a Long-Term Mutualistic Relationship with the Host To Modulate Gut Microbiota and Metabolism

Candida albicans is mostly considered an opportunistic pathogen that causes fetal systemic infections. However, this study demonstrates that in its commensal state, it maintains a long-term mutualistic relationship with the host and regulates microbial dynamics in the gut and host physiology. ABSTRACT Candida albicans survives as a commensal fungus in the gastrointestinal tract, and that its excessive growth causes infections in immunosuppressed individuals is widely accepted. However, any mutualistic relationship that may exist between C. albicans and the host remains undetermined. Here, we showed that a long-term feeding of C. albicans does not cause any noticeable infections in the mouse model. Our 16S and 18S ribosomal DNA (rDNA) sequence analyses suggested that C. albicans colonizes in the gut and modulates microbiome dynamics, which in turn mitigates high-fat-diet-induced uncontrolled body weight gain and metabolic hormonal imbalances. Interestingly, adding C. albicans to a nonobesogenic diet stimulated the appetite-regulated hormones and helped the mice maintain a healthy body weight. In concert, our results suggest a mutualism between C. albicans and the host, contrary to the notion that C. albicans is always an adversary and indicating it can instead be a bona fide admirable companion of the host. Finally, we discuss its potential translational implication as a probiotic, especially in obese people or people dependent on high-fat calorie intakes to manage obesity associated complications. IMPORTANCE Candida albicans is mostly considered an opportunistic pathogen that causes fetal systemic infections. However, this study demonstrates that in its commensal state, it maintains a long-term mutualistic relationship with the host and regulates microbial dynamics in the gut and host physiology. Thus, we concluded that C. albicans is not always an adversary but rather can be a bona fide admirable companion of the host. More importantly, as several genomic knockout strains of C. albicans were shown to be avirulent, such candidate strains may be explored further as preferable probiotic isolates to control obesity.
Machine learning-based tumor-infiltrating immune cell-associated lncRNAs for predicting prognosis and immunotherapy response in patients with glioblastoma

Long noncoding ribonucleic acids (RNAs; lncRNAs) have been associated with cancer immunity regulation. However, the roles of immune cell-specific lncRNAs in glioblastoma (GBM) remain largely unknown. In this study, a novel computational framework was constructed to screen the tumor-infiltrating immune cell-associated lncRNAs (TIIClnc) for developing TIIClnc signature by integratively analyzing the transcriptome data of purified immune cells, GBM cell lines and bulk GBM tissues using six machine learning algorithms. As a result, TIIClnc signature could distinguish survival outcomes of GBM patients across four independent datasets, including the Xiangya in-house dataset, and more importantly, showed superior performance than 95 previously established signatures in gliomas. TIIClnc signature was revealed to be an indicator of the infiltration level of immune cells and predicted the response outcomes of immunotherapy. The positive correlation between TIIClnc signature and CD8, PD-1 and PD-L1 was verified in the Xiangya in-house dataset. As a newly demonstrated predictive biomarker, the TIIClnc signature enabled a more precise selection of the GBM population who would benefit from immunotherapy and should be validated and applied in the near future.
Alpha-fetoprotein mediated targeting of polymeric nanoparticles to treat solid tumors.

Background: Serious side effects caused by paclitaxel formulation, containing toxic solubilizer Cremophor® EL, and its nonspecific accumulation greatly limit clinical paclitaxel application. Aim: To design paclitaxel-loaded copolymer of lactic and glycolic acids nanoparticles decorated with alpha-fetoprotein third domain (rAFP3d-NP) to increase paclitaxel safety profile. Methods: rAFP3d-NP was obtained via carbodiimide technique. Results: The particles were characterized with high paclitaxel loading content of 5% and size of 280 nm. rAFP3d-NP revealed biphasic profile with 67% release of paclitaxel during 220 h. Increased area under the curveinf and mean residence time values after rAFP3d-NP administration confirmed prolonged blood circulation compared with paclitaxel. rAFP3d-NP demonstrated significant tumor growth inhibition at 4T1 and SKOV-3 models. Conclusion: rAFP3d-NP is a promising delivery system for paclitaxel and can be applied similarly for delivery of other hydrophobic drugs.
Optically induced coherent transport far above Tc in underdoped YBa2Cu3O6+δ

We report on a photo-induced transient state of YBa2Cu2O6+x in which transport perpendicular to the Cu-O planes becomes highly coherent. This effect is achieved by excitation with mid-infrared optical pulses, tuned to the resonant frequency of apical oxygen vibrations, which modulate both lattice and electronic properties. Below the superconducting transition temperature Tc, the equilibrium signatures of superconducting interlayer coupling are enhanced. Most strikingly, the optical excitation induces a new reflectivity edge at higher frequency than the equilibrium Josephson plasma resonance, with a concomitant enhancement of the low frequency imaginary conductivity. Above Tc, the incoherent equilibrium conductivity becomes highly coherent, with the appearance of a reflectivity edge and a positive imaginary conductivity that increases with decreasing frequency. These features are observed up to room temperature in YBa2Cu2O6.45 and YBa2Cu2O6.5. The data above Tc can be fitted by hypothesizing that the light re-establishes a transient superconducting state over only a fraction of the solid, with a lifetime of a few picoseconds. Non-superconducting transport could also explain these observations, although one would have to assume transient carrier mobilities near 10^4 cm^2/(V.sec) at 100 K, with a density of charge carriers similar to the below Tc superfluid density. Our results are indicative of highly unconventional non-equilibrium physics and open new prospects for optical control of complex solids.
Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress.

Water availability influences all aspects of plant growth and development; however, most studies of plant responses to drought have focused on vegetative organs, notably roots and leaves. Far less is known about the molecular bases of drought acclimation responses in fruits, which are complex organs with distinct tissue types. To obtain a more comprehensive picture of the molecular mechanisms governing fruit development under drought, we profiled the transcriptomes of a spectrum of fruit tissues from tomato (Solanum lycopersicum), spanning early growth through ripening and collected from plants grown under varying intensities of water stress. In addition, we compared transcriptional changes in fruit with those in leaves to highlight different and conserved transcriptome signatures in vegetative and reproductive organs. We observed extensive and diverse genetic reprogramming in different fruit tissues and leaves, each associated with a unique response to drought acclimation. These included major transcriptional shifts in the placenta of growing fruit and in the seeds of ripe fruit related to cell growth and epigenetic regulation, respectively. Changes in metabolic and hormonal pathways, such as those related to starch, carotenoids, jasmonic acid and ethylene metabolism, were associated with distinct fruit tissues and developmental stages. Gene co-expression network analysis provided further insights into the tissue-specific regulation of distinct responses to water stress. Our data highlight the spatiotemporal specificity of drought responses in tomato fruit and indicate known and unrevealed molecular regulatory mechanisms involved in drought acclimation, during both vegetative and reproductive stages of development.
Prognostic Implications of Fractional Flow Reserve After Coronary Stenting

Key Points Question What is the clinical relevance of fractional flow reserve (FFR) after percutaneous coronary intervention (PCI) with a drug-eluting stent? Findings In this systematic review and individual patient-level meta-analysis, low post-PCI FFR was common and demonstrated a significant and inverse association with target vessel failure. This association remained consistent for the risk of cardiac death or target vessel myocardial infarction. Meaning These results support the importance of post-PCI physiologic assessment and the role of post-PCI FFR as a procedural quality metric.
Effect of capmatinib on the pharmacokinetics of substrates of CYP3A (midazolam) and CYP1A2 (caffeine) in patients with MET‐dysregulated solid tumours

Preclinical studies showed that capmatinib reversibly inhibits cytochrome P450 (CYP) 3A4 and CYP1A2 in a time‐dependent manner. In this study, we evaluated the effect of capmatinib on the exposure of sensitive substrates of CYP3A (midazolam) and CYP1A2 (caffeine) in patients with mesenchymal–epithelial transition (MET)‐dysregulated solid tumours. Besides pharmacokinetics, we assessed treatment response and safety.