Miracle-dz/UniFAR-FTUs huggingface dataset:
Applications of EPR with an Emphasis on Tau Fibril Structure

Substances containing unpaired electrons have been studied by electron paramagnetic resonance (EPR) for nearly 70 years. With continual development and enhancement of EPR techniques, questions have arisen regarding optimum method selection for a given sample based on its properties. In this work, radiation defects, natural lattice defects, solid organic radicals, radicals in solution, and spin-labeled proteins were analyzed using CW, pulse, and rapid scan EPR to compare methods. Studies of solid BDPA, E′ in quartz, Ns 0 in diamond, and a-Si:H, showed that rapid scan could overcome many obstacles presented by other techniques, cementing rapid scan as an effective alternative to CW and pulse methods. Relaxation times of six nitroxide radicals were characterized from 0.25-34 GHz, guiding synthesis of improved nitroxides for in vivo imaging experiments. Processes contributing to T1 of DPPH in polystyrene were found through variable temperature measurements at Xand Q-band, resolving previously-reported discrepancies in relaxation properties and providing new insight into this commonly-used standard. In the history of EPR, the study of proteins is relatively new. Double electronelectron resonance (DEER) has emerged as a powerful technique for the study of amyloid fibrils, a class of protein aggregates implicated in a number of neurodegenerative disorders. Microtubule-associated protein tau forms fibrils linked to Alzheimer’s disease through seeded conversion of monomer. Self-assembly is
Gastrointestinal parasitic infection in Gir Cattle (Bos primigenius indicus) and Jaffrabadi Buffalo (Bubalus bubalis) from Junagadh, Gujarat, India

Coprological analysis was performed to check the presence and previlance of gastrointestinal parasites. One hundred seventy six bovine faecal samples were studied. The study reported the presence of parasitic stages of Balantidium coli, Buxtonella sulcata, Trichostrongylus spp. , Toxocara vitulorum, Fasciola spp. , Strongyloid spp. , and Paraamphistomum spp. 43.51 % (n = 108) faecal samples from Gir cattle (Bos primigenius indicus) were positive for Gastrointestinal parasitic infections. and 36.76 % (n = 68) faecal samples from Jaffrabadi Buffaloes (Bubalus bubalis) were positive for Gastrointestinal parasitic infections. In Cattle Balantidium coli was found highest (20.37 %) and in Buffaloes Buxtonella sulcata was found highest (8.82%). the highest incidence was recorded during august for both cattle (6.48 %) and buffalo (7.35 %). Gastrointestinalparasitic infections in claves (< 12 Months) was higher than older (> 60 Months) and adult animals (12-60 Months). Season wise gastrointestinal parasitic infections in cattle were reported maximum (23.15 %) during monsoon. Maximum prevalence in buffalo was reported during Monsoon (16.18 %). similarly, females recorded higher infection rates than malesfor both cattle and buffalo.
Antimicrobial Resistance and Extended Spectrum β-Lactamases of Escherichia coli isolates from Raw Meat in Greater Accra Region, Ghana

Background Typically, raw meat can be contaminated with antimicrobial resistant pathogens at unhygienic slaughter and sale points. Consumption of meat contaminated with antimicrobial resistant E. coli is associated with grave health care consequences. The aim of this study was to determine the microbial quality of raw meat, the antimicrobial susceptibility and Extended Spectrum Beta Lactamase (ESBL) production in E. coli isolates from raw meat.Methods We collected 205 meat samples from beef (n=81), chevon (n=108) and mutton (n=16) at three slaughter sites in the Greater Accra Region of Ghana. We performed Total Plate Counts (TPC) and Total Coliform Counts (TCC) and isolated E. coli using standard bacteriological methods. Presumptive isolates were confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS). We assessed the susceptibility to 11 antibiotics using the Kirby Bauer disk diffusion method and assessed ESBL production using the combination disk test. PCR amplification of associated resistant genes bla TEM, bla SHV, and bla CTX-M was performed for presumptive ESBL isolates.Results Total Plate Counts exceeded the acceptable limit of 5.0 log CFU/ cm 2 in 60.5% (124/205) of raw meat samples. Total Coliform Counts in 70.7% (145/205) of samples were in excess of the acceptable limit of 2.5 log CFU/cm 2 . E. coli was detected in about half of raw meat samples (48%), ranging from 9.5% -79.0% among the slaughter sites. Isolates were susceptible to meropenem (100%), ceftriaxone (99%), cefotaxime (98%), chloramphenicol (97%), gentamycin (97%), ciprofloxacin (92%) and amikacin (92%), but resistant to ampicillin (57%), tetracycline (45%), sulfamethoxazole-trimethoprim (21%) and cefuroxime (17%). Multi-drug resistance (MDR) was identified in 22% of the isolates. We detected the bla TEM gene in 4% (4/98) of E. coli isolates in this study.Conclusion The levels of microbial contamination of raw meat in this study were unacceptable. Meat handlers and consumers are at risk of foodborne infections from E. coli including ESBL producing E. coli that are resistant to most antibiotics in use. We recommend an enhanced surveillance for antimicrobial resistance in food products for the early detection of emerging resistant bacteria species in the food chain.
Penerapan Pembelajaran Tematik Dalam Penanaman Moral Anak Usia Dini

Tujuan Penelitian: Bagaimanakah penerapan pembelajaran tematik untuk penanaman moral anak usia dini di Raudlatul Athfal Nurul Islam Bandar Jaya, Tanjung Jabung Timur. Metodologi: Penelitian ini merupakan penelitian deskriptif kualitatif yang bertujuan untuk menggambarkan secara objektif keadaan ditempat penelitian dengan menggunakan rangkaian kata-kata atau kalimat, dengan subjek penelitian adalah anak kelas B1 yang berjumlah 23 anak. Alat pengumpulan data yang penulis gunakan adalah observasi, wawancara dan dokumentasi. Temuan Utama: Hasil penelitian menunjukkan bahwa perkembangan pelaksanaan pembelajaran Tematik sudah cukup baik. Manfaat pembelajaran tematik dapat dilihat dari perubahan perkembangan moral anak. Perkembangan moral berkembangan dari sebelumnya karena moral anak semakin bertambah. Pelaksanaaan pembelajaran tematik dapat mengembangkan penanaman moral anak usia dini di Raudlatul Athfal Nurul Islam Bandar Jaya, Tanjung Jabung Timur cukup baik dalam mengembangkan penanaman moral anak melalui pembelajaran tematik sebagai model pembelajaran, dengan diperlukan langkah-langkah sebagai berikut: penyusunan perencanan pembelajaran, pelaksanaan pembelajaran, evaluasi pembelajaran Aplikasi dalam Penelitian: Penanam karakter sangat diperlukan menyambut kurikulum yang diajukan oleh pemerintah sekarang, maka dari itu diperlukan pembelajaran yang bisa diintegrasikan salah satunya pembelajaran tematik. Keterbarauan: Pembelajaran tematik dapat diintegrasikan untuk menunmbuhkan moral anak usia dini.
Pre-Operative Auditory-Perceptual Voice Characteristics in Patients Undergoing Thyroid and/or Parathyroid Surgery

Background: The human voice is one of the most important tools in human every day. Communication and voice were probably important to human communication even before language evolved. Voice Quality can be affected in patients with thyroid disease like, loss of vocal range, low speaking fundamental frequency (especially in women), coarse and gravelly vocal symptoms, weak voice, and breathy quality, reduced Intensity and changes of the singing voice. Purpose: The aim of this work is to identify auditory perceptual voice changes and Severity in patients with thyroid and/or parathyroid disease preoperatively. Methods: 60 adult subjects their age ranged between 20 and 60 years old, both males and females, divided into two groups were included (Group A): 30 patients diagnosed with thyroid and/or parathyroid Disease preoperatively. (Group B): 30 healthy normal subjects. Both groups were undergone to Modified GRBAS scale, Voice Recording, and Flexible nasofibrolaryngoscopy. Results: There is difference between the two groups regarding the presence or absence of dysphonia, chewing and swallowing, and parameters of APA (auditory perceptual assessment) except register. Conclusion: The perceptual measure of voice by modified GRBAS, revealed significant differences in (overall grade of dysphonia, pitch, and loudness, of voice) between the individuals with thyroid disease and those in an age and gender-matched control group. If surgeons can screen for pre-surgical dysphonia, the rate of indeterminate postsurgical dysphonia may be reduced, or at least explained and prepared for.
Data-driven Inventory Management under Customer Substitution

Most retailers that sell perishable goods offer multiple products in a product category (e.g., fresh food or fashion). Managing the inventories of these products is especially challenging due to frequent stock-outs and resulting substitution effects within the category. Furthermore, the true demand distributions of products are usually unknown to the decision maker. New digital technologies have enormously expanded the availability of data, storage capacity, and computing power and may thereby help improve inventory decisions. In this paper, we present a novel solution approach for the multi-product newsvendor problem. Our method is based on modern machine learning techniques that leverage large available datasets (e.g., data on historical sales, weather, store location, and special days) and are able to take complex substitution effects into account. We empirically evaluate our approach on two real-world datasets of a large German bakery chain. We find that our data-driven approach outperforms the model-based benchmark on the first dataset and performs competitively on the second dataset.
Optical and Theoretical Studies of Excitons in Few-Layer Lead Iodide.

Optical and Theoretical Studies of Excitons in Few-Layer Lead Iodide by Alexis S. Toulouse Chair: Roberto D. Merlin Optical measurements and first-principles calculations of few-layer lead iodide (PbI2) crystals are presented in this work. Results indicate that the band structure and exciton energies change dramatically from direct-gap bulk to few-layer PbI2. Moreover, the n = 1 exciton appears to be Frenkel-like in nature, in that its energy exhibits a weak dependence on thickness down to atomic length scales. Calculations predict large increases of the gap and exciton binding energy with decreasing number of layers, as well as a transition of the fundamental gap from direct to indirect for 1 2 layers. Results are in reasonable agreement with a simple particle-in-a-box model relying on the Wannier-Mott theory of exciton formation. General arguments and existing data suggest that the Frenkel-like character of the lowest exciton is a common feature of wide-gap layered semiconductors whose effective masses and dielectric constants yield bulk Bohr radii on the order of the layer separation. In addition, experimental observations of exciton mediated multiphonon resonant Raman scattering in few-layer PbI2 are presented. Results demonstrate that the resonance and overtone scattering strength can be tuned with varying crystal thickness. This is shown to be an effective technique for the characterization of few-layer polar semiconductors such as PbI2.
High CD38 expression in tumor-infiltrating immune cells is a favorite prognosis factor in esophageal squamous cell carcinoma with perigastric lymph node metastasis

Background The present study aimed to investigate the prognostic effect of CD38 in patients with esophageal squamous cell carcinoma (ESCC). Methods We performed a retrospective cohort study by consecutively recruiting 142 patients with ESCC. The clinicopathological features and expression of CD38, CD4, CD8, Ki-67, PD-L1 and PD-1 in tumor and immune cells were independently evaluated by two pathologists. Results CD38 was expressed in immune cells but not tumor cells and the median expression rate of CD38 in immune cells was 60%. Among ESCC patients with perigastric lymph node metastasis, the expression rate of CD38 was not associated with the disease-free survival (p = 0.207), but had a significant association with the overall survival (p = 0.042). The median overall survival was 13 months and not observed among patients with low and high expression rate of CD38, respectively. The crude and adjusted hazard ratio (HR) of high CD38 expression was 0.37 (95%CI 0.14, 0.95) and 0.21 (95%CI 0.06, 0.70). The expression rate of CD38 had a negative correlation with PD-L1 expressed in tumor cells and CD4 expressed in immune cells. Among patients without perigastric lymph node metastasis, the expression rate of CD38 showed a significant association with the disease-free survival (p < 0.05). The median disease-free survival was 45 months and not achieved for patients with high and low expression of CD38; the adjusted HR of high CD38 expression was 2.13 (95%CI 0.85, 5.33). CD38 did not have significant association with the overall survival for patients without perigastric lymph node metastasis. The expression rate of CD38 had a negative correlation with PD-L1 expressed in tumor cells and a positive correlation with PD-L1 expressed in immune cells. Conclusion The high expression rate of CD38 was associated with a better survival for ESCC with perigastric lymph node metastasis. The prognostic effect of CD38 on esophageal cancer should be warranted in future prospective studies.
Role of novel deep-learning-based CT used in management and discharge of COVID-19 patients at a “square cabin” hospital in China

Background: The chest computed tomography (CT) had been used to define the diagnostic and discharge criteria for COVID-19. However, it is difficult to determine the suitability for discharge of a patient with COVID-19 based on CT features in a clinical setting. Deep learning (DL) technology has demonstrated great success in the medical imaging.Purpose: This study applied the novel deep learning (DL) on chest computed tomography (CT) of COVID-19 patients with consecutive negative respiratory pathogen nucleic acid test results at a “square cabin” hospital in Wuhan, China, with the intent to standardize criteria for discharge.Methods: The study included 270 patients (102men, 168 women; mean age, 51.9 ± 15.6[18–65] years) who had two consecutive negative respiratory pathogen tests (sampling interval: ≥1 day) and underwent low-dose CT 1 day after the first negative test, with strict adherence to epidemic prevention standards. The chest CT of COVID-19 patients with negative nucleic acid tests were evalued by DL, and the standard for discharge was a total volume ratio of lesions to lung of less than 50% determined by DL.Results: The average intersection over union is 0.7894. Fifty-seven (21.1%) and 213 (78.9%) patients exhibited normal lung findings and pneumonia, respectively. 54.0% (115/213) involved mild interstitial fibrosis. 18.8% (40/213) had total volume ratio of lesions to lung of more than and equal to 50% according to our severity scale and were monitored continuously in hospital, and three cases of which had a positive follow-up nucleic acid test during hospital observation. None of the 230 discharged cases later tested positive or exhibited pneumonia progression. Conclusions: The novel DL enables the accurate management of COVID-19 patients and can help avoid cluster transmission or exacerbation due to patients with false negitive acid test.
Efficacy of Integrative Chinese-Western Medicine Treatments for COVID-19 Patients in ICU in Yichang, Hubei, China

BackgroundThe prognosis of severe COVID-19 patients is poor. Traditional Chinese Medicine had an advantage in keeping microenvironmental balance in treating SARS and COVID-19.MethodsThis prospective cohort study compared the efficacy and safety of integrative Chinese-Western medicine (ICWM) treatments with Western medicine (WM) treatments in severe or critically ill patients. The outcomes included: mortality, hospital stay in ICU, days with ventilator-assisted ventilation, etc.ResultsA total of 72 confirmed COVID-19 patients in ICU were included. The median age of patients was 66 years (IQR: 53-77.5), and there were 32 female patients (44.4%). There were no significant differences in laboratory tests and complications after treatments between groups. A total of 36 (50%) patients died during hospitalization, and the mortality in the ICWM group (28.6%) was significantly lower than that of the WM group (63.6%, adjusted P=0.011). And the time of assisted ventilation was shorter in the ICWM group (adjusted P=0.341). However, the median hospital stay was significantly longer in the ICWM group (18 vs. 14 days, adjusted P＜0.05). ConclusionsICWM treatments could significantly reduce mortality for severe or critically ill patients with COVID-19, and it was safe and cost-effective to add Chinese medicine.
A novel technique: hemostatic agents for port-site closure post robotic-assisted urological surgeries. a pilot study

Background: Many techniques and devices are used to close the surgical ports post minimally invasive procedures. However, they have limitations and may entail complications such as hernia, infection and dehiscence. This paper proposes novel plugging technique for port-site closure using a hemostatic agent to overcome these limitations and lower the complication rate. Objective: To assess the safety and efficacy of a novel Surgicel ® plug technique for port- site closure post minimally invasive urological surgeries. Methods: A retrospective study conducted at King Fahad Medical City/Riyadh/Saudi Arabia with 114 sample size. Patients included are those who underwent robotic assisted urological surgery (from January 2010 to December 2013) in which their port-sites were closed by the novel Surgicel ® plug technique with a minimum of 5-years follow-up period. All data were statistically analyzed using SPSS (version 23). Descriptive variables were presented as numbers and percentages. Patient demographics, type of surgery, and follow-up results. Results: A total of 114 patients were collected. 50 were males with a mean age of 41.9 (SD=18.2) and 64 were females with a mean age of 39.2 (SD=18.3). The male-female ratio is 1:1.2. In total, two cases (1.7%) developed port-site non-infectious discharge during radical nephrectomy and pyeloplasty, and one case (0.8%) developed port-site hernia during ureteric reimplantation. 111 cases (97.3%) had no port-site complications. Conclusion: This study showed that the novel plugging technique of port-site closure post minimally invasive urological procedures using a hemostatic agent (Surgicel ® ) is feasible, safe, easy, and effective in the group of patients studiedand could be considered as a newapproachfor trocar sites closure.
Salmonella Phage cocktail, its effects and benefits on the gut of chickens in a commercial farm.

BackgroundThe microbiota of broiler chicken gut affects positively or negatively the health, metabolism and immunity of chickens thus it has a significant impact on the animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The aim of the study is further characterizing the behaviour of phages and its effect on the commensal microbial community.MethodsWe used 16S rRNA gene amplicon sequencing to evaluate the effect of SalmoFree® (a phage cocktail against Salmonella) on the microbiota of the cecum of broilers reared in a commercial farming system. Two field trials were carried out including 2 control and 2 experimental houses. Phages were incorporated in the broilers’ drinking water using three doses at the grower stage. The core microbiome, differentially abundant taxa between treatments as well as taxa associated with age were identified using Qiime2 and the R-Project for statistics.ResultsAnalyses of similarities among communities over time allowed us to identify two stages of microbiota development at the last stage of the production cycle. The core microbiome identified some key species in the adaptation of the microbiota at the last stage of the cycle. Among these there are important degraders of complex polysaccharides and producers of short chain fatty acids such as Eisenbergiella and Lachnoclostridium. Additionally, the phage cocktail did not affect the normal development of the microbiota structure while its application contributes to reduce the presence of pathogenic Enterobacteria including Salmonella. The addition of the phage cocktail led to a significant reduction in the abundance of Campylobacter and Helicobacter and increase in Butyricimonas and Rikenellaceae abundance which are common inhabitants of the chicken gut with known negative and positive effects in the health, respectively.ConclusionsOur results suggest that phages can contribute to improve the chicken health and reduce pathogens burden at the end of the production cycle of broilers. Furthermore, it presents for the first time a detailed look of the microbiota composition and changes in broilers in a commercial scenario, information that will valuable towards the implementation of phage therapy technologies in the field.
The miRNA-gene regulatory circuits in nSARS-CoV-2 and their potential correlations with pulmonary and thrombotic disorders

In view of the worldwide spread of the novel Severe Acute Respiratory Syndrome Coronavirus 2 (nSARS-CoV-2) infection pandemic situation, research to repurpose drugs, identify novel drug targets, vaccine candidates, diagnostic markers etc have created a new race to curb the disease. To uncover nSARS-CoV-2-related important biological features and understanding the molecular basis of this disease, network biology and miRNA-gene regulatory motif-based approach is used. 11 antiviral human-microRNAs (miRNAs) which can potentially target SARS-CoV-2 genes were collated; their direct miRNA interactors were identified and a comprehensive nSARS-CoV-2 responsive miRNA:Transcription Factor (TF):gene coregulatory network was built. 1385 miRNA:TF:gene tripartite, Feed-Forward Loops (FFLs) were identified from the network. The network topology was mapped into the biological space and the overrepresented pathways were identified. Four regulatory circuits: hsa-mir-9-5p-EP300-PLCB4, hsa-mir-324-3p-MYC-HLA-F, hsa-mir-1827-E2F1-CTSV and hsa-mir-1277-5p-SP1-CANX are identified. These miRNA-gene regulatory circuits are found to regulate signalling pathways like virus endocytosis, viral replication, inflammatory response, pulmonary vascularization, cell cycle control, virus spike protein stabilization, antigen presentation, etc. Some novel computational evidences for understanding nSARS-CoV-2 molecular mechanisms controlled by these regulatory circuits is put forth. The novel associations of miRNAs and genes identified with this infection are open for experimental validation. Further, these regulatory circuits also suggest potential correlations/similarity in the molecular mechanisms during nSARS-CoV-2 infection and pulmonary diseases and thromboembolic disorders. A detailed molecular snapshot of TGF-β signalling pathway as the common mechanism that could play an important role in controlling common pathophysiology i.e. systemic inflammation, increased pulmonary pressure, ground glass opacities, D-dimer overexpression is also put forth.