Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing Extensive Semi-Arid Rangeland Beef Cow–Calf Welfare in Namibia: Part 1: Comparison between Farm Production System’s Effect on the Welfare of Beef Cows

Simple Summary Namibia is in the process of updating animal welfare legislation. This needs to include an assessment protocol for beef cattle production systems that is sufficiently rigorous for the country to gain and maintain access to high-value beef export markets. Beef is produced in commercial and semi-commercial systems and in communal village farms. Privately owned commercial farms allow maximum herd and rangeland management to ensure optimum productivity and profitability. Village farms (semi-commercial and communal) have limited grazing land, with consequent challenges of grazing and water management, as well as traditional customs of cattle management. A protocol was developed to assess the welfare of beef cattle in the context of these production systems. The application of the welfare assessment protocol indicated that the standards of welfare differed across production systems, with commercial farms achieving the best standard of welfare, followed by semi-commercial, then communal village farms. The greatest opportunity for change exists within the semi-commercial village farms, which need to attain to the requirements imposed by international markets to maximize their returns; hence herd management and welfare status is better than in the purely communal farms. This suggests that commercialization of communal farming may have benefits for animal welfare. Abstract A proposed animal welfare assessment protocol for semi-arid rangeland-based cow–calf systems in Namibia combined 40 measures from a protocol developed for beef cattle in New Zealand with additional Namibia-specific measures. Preliminary validation of the protocol had been undertaken with five herds in one semi-commercial village. The aim of the current study was to apply this protocol and compare animal welfare across three cow–calf production systems in Namibia. A total of 2529 beef cows were evaluated during pregnancy testing in the yards of 17 commercial, 20 semi-commercial, and 18 communal (total: 55) herds followed by an assessment of farm resources and a questionnaire-guided interview. Non-parametric tests were used to evaluate the difference in the welfare scores between the production systems. The results indicated a discrepancy of animal welfare between the three farm types, with a marked separation of commercial farms from semi-commercial, and communal village farms in the least. The differences in these production systems were mainly driven by economic gains through access to better beef export market for commercial farms and semi-commercial villages, as well as by the differences in the available grazing land, facility designs/quality, and traditional customs in the village systems. The results indicate an advantage of commercialization over communalization.
Maize Endosperm Development.

Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental program. The high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed development. Detailed spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments: the basal endosperm transfer layer (BETL), aleurone layer (AL), starchy endosperm (SE), and embryo-surrounding region (ESR). Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary, there have been some exciting advances, such as the identification of OPAQUE11 (O11) as a central hub of the maize endosperm regulatory network connecting endosperm development, nutrient metabolism, and stress responses, and the discovery that the endosperm adjacent to scutellum (EAS) serves as a dynamic interface for endosperm-embryo crosstalk. In addition, several genes that function in BETL development, AL differentiation, and the endosperm cell cycle have been identified, such as ZmSWEET4c, Thk1, and Dek15, respectively. Here, we focus on current advances in understanding the molecular factors involved in BETL, AL, SE, ESR, and EAS development, including the specific transcriptional regulatory networks that function in each compartment during endosperm development. This article is protected by copyright. All rights reserved.
Identification of Cathepsin D as a Plasma Biomarker for Alzheimer’s Disease

Although Alzheimer’s disease (AD) is the most common neurodegenerative disease, there are still no drugs available to treat or prevent AD effectively. Here, we examined changes in levels of selected proteins implicated in the pathogenesis of AD using plasma samples of control subjects and patients with cognition impairment. To precisely categorize the disease, fifty-six participants were examined with clinical cognitive tests, amyloid positron emission tomography (PET) scan, and white matter hyperintensities scored by magnetic resonance imaging. Plasma cathepsin D levels of the subjects were examined by immunoblotting and enzyme-linked immunosorbent assay (ELISA). Correlation of plasma cathepsin D levels with AD-related factors and clinical characteristics were examined by statistical analysis. By analyzing quantitative immunoblot and ELISA, we found that the plasma level of cathepsin D, a major lysosomal protease, was decreased in the group with amyloid plaque deposition at the brain compared to the control group. The level of plasma cathepsin D was negatively correlated with clinical dementia rating scale sum of boxes (CDR-SB) scores. In addition, our integrated multivariable logistic regression model suggests the high performance of plasma cathepsin D level for discriminating AD from non-AD. These results suggest that the plasma cathepsin D level could be developed as a diagnostic biomarker candidate for AD.
Hocheffiziente photolabile Schutzgruppen mit intramolekularem Energietransfer

DNA-Chips werden in stark zunehmendem Mase in der Genomanalytik eingesetzt. Inzwischen k"nnen hochdichte DNA-Chips mit einigen Hunderttausend verschiedener Punkte (Spots) pro cm hergestellt werden. Damit l*sst sich im Prinzip das gesamte menschliche Genom erfassen. Solch hohe Punktdichten erzielt man durch eine photolithographische In-situ-DNA-Chip-Synthese. Hierbei werden die Oligonucleotide schrittweise aus gesch/tzten Nucleosidphosphitamiden mit Photolithographie durch Masken oder Mikrospiegel-Anordnungen r*umlich definiert aufgebaut. Diese Technik erfordert photolabile Schutzgruppen mit hoher Lichtempfindlichkeit, die ihr Substrat (in diesem Fall ein Nucleotid) in nahezu quantitativen Ausbeuten freisetzen. Eine charakteristische Maszahl f/r die Lichtempfindlichkeit stellt das Produkt ef aus Absorptionskoeffizient und Quantenausbeute dar; es erreicht bei den bisher f/r die DNAChip-Synthese /blichen Schutzgruppen nur m*sige Werte. Die [(a-Methyl-2-nitropiperonyl)oxy]carbonyl(MeNPOC)Schutzgruppe weist bei den praktisch eingesetzten Wellenl*ngen (vorzugsweise wird die Quecksilberlinie bei l= 366 nm verwendet) zwar einen akzeptablen Absorptionskoeffizienten auf (eMeOH,366 nm 2500m 1 cm ), jedoch ist die Quantenausbeute f/r die Entsch/tzung sehr gering (3% in MeOH). Im Unterschied dazu zeigt die 2-(2-Nitrophenyl)propoxycarbonyl(NPPOC)-Schutzgruppe, deren Reaktion in Schema 1 dargestellt ist, eine wesentlich h"here
Tobacco, alcohol use and other risk factors for developing symptomatic COVID-19 vs asymptomatic SARS-CoV-2 infection: a case-control study from western Rajasthan, India.

BACKGROUND Understanding risk factors of symptomatic coronavirus disease 2019 (COVID-19) vis-à-vis asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, severe disease and death is important. METHODS An unmatched case-control study was conducted through telephonic interviews among individuals who tested positive for SARS-CoV-2 in Jodhpur, India from 23 March to 20 July 2020. Contact history, comorbidities and tobacco and alcohol use were elicited using standard tools. RESULTS Among 911 SARS-CoV-2-infected individuals, 47.5% were symptomatic, 14.1% had severe COVID-19 and 41 (4.5%) died. Older age, working outside the home, cardiac and respiratory comorbidity and alcohol use were found to increase the risk of symptomatic disease as compared with asymptomatic infection. Current tobacco smoking (odds ratio [OR] 0.46 [95% confidence interval {CI} 0.26 to 0.78]) but not smokeless tobacco use (OR 0.81 [95% CI 0.55 to 1.19]) appeared to reduce the risk of symptomatic disease. Age ≥60 y and renal comorbidity were significantly associated with severe COVID-19. Age ≥60 y and respiratory and cardiac comorbidity were found to predispose to mortality. CONCLUSIONS The apparent reduced risk of symptomatic COVID-19 among tobacco smokers could be due to residual confounding owing to unknown factors, while acknowledging the limitation of recall bias. Cross-protection afforded by frequent upper respiratory tract infection among tobacco smokers could explain why a similar association was not found for smokeless tobacco use, thereby being more plausible than the 'nicotinic hypothesis'. Those with comorbidities and age ≥60 y should be prioritized for hospital admission.
SurVirus: a repeat-aware virus integration caller

Abstract A significant portion of human cancers are due to viruses integrating into human genomes. Therefore, accurately predicting virus integrations can help uncover the mechanisms that lead to many devastating diseases. Virus integrations can be called by analysing second generation high-throughput sequencing datasets. Unfortunately, existing methods fail to report a significant portion of integrations, while predicting a large number of false positives. We observe that the inaccuracy is caused by incorrect alignment of reads in repetitive regions. False alignments create false positives, while missing alignments create false negatives. This paper proposes SurVirus, an improved virus integration caller that corrects the alignment of reads which are crucial for the discovery of integrations. We use publicly available datasets to show that existing methods predict hundreds of thousands of false positives; SurVirus, on the other hand, is significantly more precise while it also detects many novel integrations previously missed by other tools, most of which are in repetitive regions. We validate a subset of these novel integrations, and find that the majority are correct. Using SurVirus, we find that HPV and HBV integrations are enriched in LINE and Satellite regions which had been overlooked, as well as discover recurrent HBV and HPV breakpoints in human genome-virus fusion transcripts.
1′-Acetoxychavicol Acetate from Alpinia galanga Represses Proliferation and Invasion, and Induces Apoptosis via HER2-signaling in Endocrine-Resistant Breast Cancer Cells

Abstract Estrogen receptor-positive breast cancer patients have a good prognosis, but 30% of these patients will experience recurrence due to the development of resistance through various signaling pathways. This study aimed to evaluate the mode of anticancer effects of 1′-acetoxychavicol acetate, which is isolated from the rhizomes of Alpinia galanga in estrogen receptor positive (MCF7) human epidermal growth factor receptor 2-overexpressed (MCF7/HER2), and endocrine-resistant breast cancer cells (MCF7/LCC2 and MCF7/LCC9). 1′-Acetoxychavicol acetate showed antiproliferation in a concentration- and time-dependent fashion and had higher potency in human epidermal growth factor receptor 2-overexpressed cell lines. This was associated with down-regulation of human epidermal growth factor receptor 2, pERK1/2, pAKT, estrogen receptor coactivator, cyclin D1, and MYC proto-oncogene while in vivo and significant reduction in the tumor mass of 1′-acetoxychavicol acetate-treated zebrafish-engrafted breast cancer groups. The anti-invasive effects of 1′-acetoxychavicol acetate were confirmed in vitro by the matrigel invasion assay and with down-regulation of C – X-C chemokine receptor type 4, urokinase plasminogen activator, vascular endothelial growth factor, and basic fibroblast growth factor 2 genes. The down-regulation of urokinase plasminogen activator and fibroblast growth factor 2 proteins was also validated by molecular docking analysis. Moreover, 1′-acetoxychavicol acetate-treated cells exhibited lower expression levels of the anti-apoptotic Bcl-2 and Mcl-1 proteins in addition to enhanced stress-activated kinases/c-Jun N-terminal kinase 1/2 and poly-ADP ribose polymerase cleavage, indicating apoptotic cell induction by 1′-acetoxychavicol acetate. Moreover, 1′-acetoxychavicol acetate had higher potency in human epidermal growth factor receptor 2-overexpressed cell lines regarding its inhibition on human epidermal growth factor receptor 2, pAKT, pERK1/2, PSer118, and PSer167-ERα proteins. Our findings suggest 1′-acetoxychavicol acetate mediates its anti-cancer effects via human epidermal growth factor receptor 2 signaling pathway.
Impact of anticoagulation strategy after left atrial appendage occlusion in patients requiring direct current cardioversion

Current guidelines recommend adequate anticoagulation for at least 3 weeks pre‐ and 4 weeks post‐direct current cardioversion (DCCV) to reduce thrombo‐embolic risk in patients with atrial fibrillation (AF) lasting greater than 48 h. No specific recommendations exist for DCCV in patients that have undergone left atrial appendage occlusion (LAAO), many of whom are ineligible for anticoagulation. This study aims to observe the efficacy and safety of DCCV post‐LAAO in everyday clinical practice.
Electrostatic interactions for directed assembly of nanostructured materials: composites of titanium dioxide nanotubes with gold nanoparticles

Interactions of titanium dioxide nanotubes (TiO2NTs) with positively (AuNP+s) and negatively charged (AuNP−s) gold nanoparticles have been investigated using a combination of UV-Vis spectroscopy, ζ potential and transmission electron microscopy analyses. Possessing a negatively charged surface, TiO2NTs show no attractive interactions with AuNP−s, but readily form nanostructured composites with AuNP+s. Using different ratios of TiO2NT : AuNP+, the overall charge of nanotube–nanoparticle composite can be tuned from positive through neutral to negative, which drastically affects the solubility of the resultant material in water. The charge of the nano-composite is related to the density of AuNP+s adsorbed on the surface of the TiO2NTs. At higher densities adsorbed nanoparticles interact with each other and exhibit a red-shift of their surface plasmon resonance, the magnitude of which increases with the density of AuNP+s. This methodology enables precise control over the composition, charge and structure of nanotube–nanoparticle materials.
Hallux Varus Correction With Extensor Hallucis Longus Tendon Transfer and Reverse Scarf Osteotomy

Introduction Hallux varus is the medial deviation of the hallux. Although rare, it can cause discomfort, functional weakness, difficulty with shoe wear, and dissatisfactory cosmesis. This study reports 3 cases of hallux varus treated using extensor hallucis longus (EHL) tendon transfer with or without the use of reverse scarf osteotomy (RSO). Methods This cases series studies the technique of using EHL tendon transfer and the role for RSO in the surgical correction of hallux varus. Indication for RSO included osseous overcorrection in the index hallux valgus surgery or as an adjunct when EHL tendon transfer alone was unable to restore alignment. Patients were followed-up for 24 months and their postoperative outcomes were recorded. Results All patients were female between the ages 55 to 67 years. Radiological parameters after surgery improved in all patients. The mean hallux-valgus angle was corrected from −23.7 ± 3.5° to −3.2 ± 2.0° postoperatively ( P < .05). Intermetatarsal angle was increased from 5.0 ± 1.9° to 6.7 ± 1.0° ( P = .065). Distal metatarsal articular angle improved from −28.9 ± 7.6° to −7.8 ± 3.7° ( P < .05). Mean American Orthopaedic Foot and Ankle Society scores improved from 37 ± 24 to 75 ± 9 ( P = .064) at 24 months. In addition, visual analogue scale pain scores reduced from 5 ± 1.5 to 1 ± 1 ( P < .05). All patients reported being satisfied with the procedure, and no complications were reported at 24 months after surgery. Conclusion Hallux varus correction using EHL tendon transfer with or without RSO appears to provide satisfactory results at 24 months. Levels of Evidence Level V: Expert opinion, Techniques
Deep learning for intelligent diagnosis in thyroid scintigraphy

Objective To construct deep learning (DL) models to improve the accuracy and efficiency of thyroid disease diagnosis by thyroid scintigraphy. Methods We constructed DL models with AlexNet, VGGNet, and ResNet. The models were trained separately with transfer learning. We measured each model’s performance with six indicators: recall, precision, negative predictive value (NPV), specificity, accuracy, and F1-score. We also compared the diagnostic performances of first- and third-year nuclear medicine (NM) residents with assistance from the best-performing DL-based model. The Kappa coefficient and average classification time of each model were compared with those of two NM residents. Results The recall, precision, NPV, specificity, accuracy, and F1-score of the three models ranged from 73.33% to 97.00%. The Kappa coefficient of all three models was >0.710. All models performed better than the first-year NM resident but not as well as the third-year NM resident in terms of diagnostic ability. However, the ResNet model provided “diagnostic assistance” to the NM residents. The models provided results at speeds 400 to 600 times faster than the NM residents. Conclusion DL-based models perform well in diagnostic assessment by thyroid scintigraphy. These models may serve as tools for NM residents in the diagnosis of Graves’ disease and subacute thyroiditis.
Clinical Considerations for a Family with Dilated Cardiomyopathy, Sudden Cardiac Death, and a Novel TTN Frameshift Mutation

Dilated cardiomyopathy (DCM) is the leading indication for heart transplantation. TTN gene truncating mutations account for about 25% of familial DCM cases and for 18% of sporadic DCM cases. The clinical relevance of specific variants in TTN has been difficult to determine because of the sheer size of the protein for which TTN encodes, as well as existing extensive genetic variation. Clinicians should communicate novel clinically-relevant variants and genotype–phenotype associations, so that animal studies evaluating the molecular mechanisms are always conducted with a focus on clinical significance. In the present study, we report for the first time the novel truncating heterozygous variant NM_001256850. 1:c. 72777_72783del (p.Phe24259Leufs*51) in the TTN gene and its association with DCM in a family with sudden death. This variant occurs in the A-band region of the sarcomere, in a known mutational hotspot of the gene. Truncating titin variants that occur in this region are the most common cause of DCM and have been rarely reported in asymptomatic individuals, differently from other pathogenic TTN gene variants. Further studies are warranted to better understand this particular clinically-relevant variant.
Scoring model of convex probe endobronchial ultrasound multimodal imaging in differentiating benign and malignant lung lesions

Background Convex probe endobronchial ultrasound images can reflect the morphology, blood flow status and stiffness of the lesions. Endobronchial ultrasound multimodal imaging has great value for the diagnosis of intrathoracic lymph nodes. This study aimed to analyze the application of endobronchial ultrasound multimodal imaging on lung lesions. Methods Patients undergoing endobronchial ultrasound-guided transbronchial needle aspiration in Shanghai Chest Hospital from July 2018 to December 2019 were retrospectively enrolled. Nine grayscale features (long and short axes, margin, shape, lobulation sign, echogenicity, necrosis, liquefaction, calcification, and air-bronchogram), blood flow volume and elastography five-score method were analyzed to explore the best diagnostic method. The gold standard for diagnosing lesions depends on the histological and cytopathological findings of endobronchial ultrasound-guided transbronchial needle aspiration, transthoracic biopsy, resected sample of lesions, microbiological examination or clinical follow-up of at least 6 months. Results Endobronchial ultrasound multimodal imaging of 97 malignant lung lesions and 19 benign lung lesions from 116 patients were analyzed. There were statistically significant differences in distinct margin, presence of lobulation sign, presence of necrosis, and elastography grading score 4–5 between malignant and benign lung lesions, among which presence of lobulation sign and elastography grading score 4–5 were independent predictors. A diagnostic scoring model was then constructed based on the above four features, and when two or more features were present, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy for malignant lung lesions prediction were 92.78%, 57.89%, 91.84%, 61.11% and 87.07%, respectively. Conclusions The combination of endobronchial ultrasound grayscale and elastography has potential value for malignant and benign lung lesions differentiation. The diagnostic scoring model established in this study needs further validation to guide the malignant and benign diagnosis of lung lesions.
X-ray diffraction of multilayers and superlattices

Recursion formulae for calculating the reflected amplitude ratio of multilayers and superlattices have been derived from the Takagi-Taupin differential equations, which describe the dynamical diffraction of X-rays in deformed crystals. Calculated rocking curves of complicated layered structures, such as non-ideal superlattices on perfect crystals, are shown to be in good agreement with observed diffraction profiles. The kinematical theory can save computing time only in the case of an ideal superlattice, for which a geometric series can be used, but the reflectivity must be below 10% so that multiple reflections can be neglected. For a perfect crystal of arbitrary thickness the absorption at the center of the dynamical reflection is found to be proportional to the square root of the reflectivity. Sputter-deposited periodic multilayers of tungsten and carbon can be considered as an artificial crystal, for which dynamical X-ray diffraction calculations give results very similar to those of a macroscopic optical description in terms of the complex index of refraction and Fresnel reflection coefficients.
Improvement In Flowability And Compressibility Of Ampicillin Trihydrate By Spherical Crystallization

Spherical crystallization was carried out by ammonia diffusion method to achieve agglomerates of primary crystals of the drug. Both agglomerated and primary crystals were subjected to measurement of micromeritic properties, compressibility, powder compaction properties and effect of crystal shape on tablet strength. Dispersible tablets of agglomerated ampicillin trihydrate were prepared using suitable excipients in formula and were evaluated for various physical parameters.The tablets gave comparable drug release with that obtained from a market product.