Miracle-dz/UniFAR-FTUs huggingface dataset:
Behavior, health, and productivity of early-lactation dairy cows supplemented with molasses in automated milking systems.

The objective of this study was to determine the effect of molasses-based liquid feed (LF) supplementation within automated milking systems (AMS) on the behavior, health, and production of early-lactation dairy cows. In 6 commercial AMS dairy herds, 390 dairy cows were randomly assigned before calving to 1 of 2 treatments, within farm, balanced by parity: (1) control group (CON) receiving a standard AMS pellet [mean = 3.9 kg/d on a dry matter (DM) basis, n = 188], or (2) same amount of standard AMS pellet (mean = 3.6 kg/d on a DM basis, n = 202) plus 1 kg/d DM of LF for multiparous cows (1.6 kg/d as fed) and 0.88 kg/d DM for primiparous cows (1.4 kg/d as fed). Across farms, cows were fed partial mixed rations similar in ingredient and nutrient composition. Cows on the LF treatment received supplementation for the first 60 d in milk (DIM). Blood samples were taken 2 times/wk for the first 3 wk postcalving to assess β-hydroxybutyrate (BHB). Samples with BHB ≥1.2 mmol/L were classified as a positive case of subclinical ketosis (SCK). Cow body condition and lameness were scored every 10 d postcalving until 60 DIM. No differences were detected between treatments for milk yield (average milk yield = 37.4 ± 1.98 kg/d) and milking frequency (average milking frequency = 3.2 ± 0.01 times/d). Similarly, no difference between treatments in daily AMS visits was detected (average AMS visits = 5.3 ± 0.3 times/d). However, CON cows experienced more AMS refusals/d than LF cows (LF = 1.6 refusals/d, CON = 2.1 refusals/d). No difference between treatments in daily rumination time was detected (average rumination time = 476 ± 10.8 min/d). Treatment was associated with the number of times cows tested positive for SCK; cows on LF had fewer repeated diagnoses of SCK, such that 15% of cows on LF had ≥3 diagnoses of SCK out of 5 tests, compared with 27% of CON cows. Cows receiving molasses tended to have lower blood BHB values at ~15 DIM. Molasses supplementation also allowed cows to maintain a more stable body condition score, as LF cows tended to lose less body condition over the first 60 DIM compared with CON cows. Overall, the results of this study demonstrate that supplementing a molasses-based LF to AMS cows may help support the energy demands of milk production in early lactation and, thus, reduce the incidence of repeat positive SCK tests during that time period.
Alpha lipoic acid attenuates iron induced oxidative acute kidney injury in rats

ABSTRACT Iron has been implicated in oxidative tissue injury owing to its ability to generate reactive oxygen species (ROS). We investigated the reno-protective effects of alpha lipoic acid (ALA) by investigating its effects on the kidney isoform of NADPH oxidase (Nox4) and the specific signaling pathways, p38 MAPK and PI3K/Akt, which participate in apoptosis and survival, respectively. We established four groups of seven rats: control, 100 mg/kg ALA, 80 mg/kg iron sucrose (IS) and IS + ALA. IS and ALA were injected intravenously and rats were sacrificied after 6 h. The mRNA expression of the subunits of NADPH oxidase, Nox4 and p22phox; tumor necrosis factor-alpha (TNF-α); and kidney injury molecule-1 (KIM-1) were measured using quantitative real time polymerase chain reaction (qRT-PCR). Active caspase-3 protein expression was evaluated by immunostaining. Also, p38 MAPK and PI3K/Akt signaling pathways were analyzed using western blot. ALA suppressed the mRNA expression of Nox4, p22phox, TNF-α and KIM-1. Active caspase-3 protein expression induced by IS was decreased by ALA. ALA also suppressed p38 MAPK and activated the PI3K/Akt signaling pathway following IS administration. We found that ALA may be an effective strategy for preventing oxidative acute kidney injury caused by IS.
Oncologist Confidence in Genomic Testing and Implications for Using Multimarker Tumor Panel Tests in Practice

PURPOSE The evolution of precision oncology increasingly requires oncologists to incorporate genomic testing into practice. Yet, providers’ confidence with genomic testing is poorly documented. This article describes medical oncologists’ confidence with genomic testing and the association between genomic confidence and test use. METHODS We used data from the 2017 National Survey of Precision Medicine in Cancer Treatment to characterize oncologists’ confidence with genomic testing. Genomic confidence was examined separately by type of test user: next-generation sequencing (NGS) only, gene expression (GE) only, both NGS and GE, or nonuser. Predictors of genomic confidence were examined with multinomial logistic regression. The association between genomic confidence and test use was examined with multivariable linear regression. RESULTS More than 75% of genomic test users were either moderately or very confident about using results from multimarker tumor panel tests to guide patient care. Confidence with using multimarker tumor panel tests was highest among both NGS and GE test users, with 60.1% very confident in using test results, and lowest among NGS-only test users, with 38.2% very confident in using test results. Oncologists were most confident in using single-gene tests and least confident in using whole-genome or -exome sequencing to guide patient care. Genomic confidence was positively associated with self-reported test use. In adjusted models, training in genomics, larger patient volume, and treating patients with solid tumors predicted higher genomic confidence. Onsite pathology services and receipt of electronic medical record alerts for genomic testing predicted lower genomic confidence. CONCLUSION Oncologists’ confidence varies by testing platform, patient volume, genomic training, and practice infrastructure. Research is needed to identify modifiable factors that can be targeted to enhance provider confidence with genomic testing.
Cannabis Extracts Affected Metabolic Syndrome Parameters in Mice Fed High-Fat/Cholesterol Diet.

Introduction: Nonalcoholic fatty liver disease (NAFLD) is associated with metabolic syndrome, which often includes obesity, diabetes, and dyslipidemia. Several studies in mice and humans have implicated the involvement of the gut microbiome in NAFLD. While cannabis may potentially be beneficial for treating metabolic disorders such as NAFLD, the effects of cannabis on liver diseases and gut microbiota profile are yet to be addressed. In this study, we evaluated the therapeutic effects of cannabis strains with different cannabinoid profiles on NAFLD progression. Materials and Methods: NAFLD was induced by feeding mice a high-fat/cholesterol diet (HFCD) for 6 weeks. During this period, cannabis extracts were administrated orally at a concentration of 5 mg/kg every 3 days. Profile of lipids, liver enzymes, glucose tolerance, and gene expression related to carbohydrate lipid metabolism and liver inflammation were analyzed. The effect of cannabis strains on microbiota composition in the gut was evaluated. Results: A cannabidiol (CBD)-rich extract produced an increase in inflammatory related gene expression and a less diverse microbiota profile, associated with increased fasting glucose levels in HFCD-fed mice. In contrast, mice receiving a tetrahydrocannabinol (THC)-rich extract exhibited moderate weight gain, improved glucose response curves, and a decrease in liver enzymes. Conclusions: The results of this study indicate that the administration of cannabis containing elevated levels of THC may help ameliorate symptoms of NAFLD, whereas administration of CBD-rich cannabis extracts may cause a proinflammatory effect in the liver, linked with an unfavorable change in the microbiota profile. Our preliminary data suggest that these effects are mediated by mechanisms other than increased expression of the endocannabinoid receptors cannabinoid receptor 1 (CB1) and CB2.
Surgical Treatment for Left Main Coronary Atresia with Significant Mitral Regurgitation in a 1-Year-Old Child

Congenital atresia of the left main coronary artery (LMCA) is an extremely rare coronary anomaly that necessitates surgical correction. Patients with LMCA atresia may have various clinical symptoms, which are determined by the degree of collateral vessel development from the right coronary system, the metabolic demands of the heart, and concomitant mitral insufficiency caused by myocardial ischemia. Unlike in adults, there are limited surgical options for coronary artery disease in children. Herein, we report a case of LMCA atresia with mitral regurgitation in a 19-month-old child that was successfully corrected by coronary artery bypass grafting and mitral valve repair.
Immune response in common carp (Cyprinus carpio L.) following glyphosate-exposure

Abstract In this study, we aimed to evaluate the effects of glyphosate on the lysozyme (LYZ), immunoglobulin M (IgM) and complement C3 (C3) in the liver and spleen of common carp following 52.08 or 104.15 mgL−1 of glyphosate exposure for 1 and 7 d, respectively. The results showed that both LYZ transcription and activity were suppressed in the liver and spleen from the glyphosate-treated fish at the end of test. Moreover, glyphosate exposure also altered the transcription or content of IgM and C3 in the liver and spleen from the treated fish. These results indicate that glyphosate exert immunotoxicity on common carp.
Ex vivo imaging immune cell interactions in T cell vaccine-induced immunity and CD8+CD25+ T regulatory cell-mediated immune suppression

III TABLE OF CONTENTS . VI LIST OF FIGURES . XI LIST OF TABLE . XIII LIST OF ABBREVIATIONS . XIV CHAPTER 1 LITERATURE REVIEWS . 1 1.1 CELLS OF THE IMMUNE SYSTEM . 1 1.1.1 Overview of immune responses . 1 1.1.2 DC subsets . 2 1.1.2.1 Conventional steady-state DCs . 2 1.1.2.2 Non-conventional DCs. 4 1.1. 3 CD4 + T lymphocyte subsets . 5 1.1. 3.1 Th1 and Th2 cells. 6 1.1. 3.2 Th17 cells . 7 1.1. 3.3 Regulatory CD4 + T cells . 7 1.1. 3.4 Follicular helper (Tfh) T cells. 8 1.1. 3.5 More CD4 + T-cell subsets: Th9 and Th22 cells . 8 1.1. 4 CD8 + T lymphocytes . 8 1.1. 5 Summary . 9 1.2 EXOSOME (EXO)-DERIVED VACCINES . 9 1.2.1 EXO biogenesis and composition . 9 1.2.2 EXO biological functions . 11 1.2.2.1 Elimination of obsolete proteins . 11 1.2.2.2 Intercellular communication . 11 1.2. 3 Modulation of immune responses . 12
MiR‐95‐5p involves in the migration and invasion of trophoblast cells by targeting low density lipoprotein receptor‐related protein 6

Low density lipoprotein receptor‐related protein 6 (LRP6) has been demonstrated to control trophoblast cell invasion, but its regulatory gene remains undefined. In this study, microRNA (miR) regulating LRP6 were explored to elucidate the potential mechanism of preeclampsia (PE).
Cloning and expression vector construction of Arabidopsis NPR1 gene

The Arabidopsis NPR1 gene plays an important role in activating various plant defense responses,including expression of the pathogenesis-related genes and systemic acquired resistance. The NPR1 gene was amplified from Arabidopsis thaliana genome DNA by DNA-PCR method. The DNA sequenced analysis showed that the sequence of amplified NPR1 gene was the same as the published sequence. Therefore, the plant expression vector pCaMVNPR containing NPR1 gene was constructed. The experiment will provide avenues for NPR1 gene application in plant disease resistant genetic engineering.
Morphological basis of glossy red plumage colours

Brightly coloured feathers, including the brilliant reds produced by carotenoids, are sometimes shiny in appearance. Gloss is a common property of materials and usually arises through specular reflection from smooth, flat surfaces. However, the production of gloss on red feathers has never been examined. In the present study, we compared the optical and structural properties of glossy and matte carotenoid-based red feathers of multiple species to identify the proximate basis for their glossiness. Although specular reflectance did not differ between glossy and matte feathers, diffuse reflectance was lower in glossy than in matte feathers, leading to a higher contrast gloss. Compared to matte feathers, glossy red feathers had thicker barbs with a flatter and more homogeneous morphology, consistent with expectations, as well as thicker outer keratin cortices. Moreover, glossiness was predicted by a principal component regression using these same morphological traits. We demonstrate that the gloss of carotenoid-based red feathers is produced at least in part by a smooth, flattened barb microstructure and an enhanced nanostructure, illustrating a novel colour-producing interaction that neither pigment, nor microstructure could alone attain. How the ecology and evolution of species with glossy red feather differ from those with typical matte red feathers represent rich areas for future study.
Five-component model validation of reference, laboratory and field methods of body composition assessment

Abstract This study reports the validity of body fat percentage (BF%) estimates from several commonly employed techniques as compared with a five-component (5C) model criterion. Healthy adults (n 170) were assessed by dual-energy X-ray absorptiometry (DXA), air displacement plethysmography (ADP), multiple bioimpedance techniques and optical scanning. Output was also used to produce a criterion 5C model, multiple variants of three- and four-component models (3C; 4C) and anthropometry-based BF% estimates. Linear regression, Bland–Altman analysis and equivalence testing were performed alongside evaluation of the constant error (CE), total error (TE), se of the estimate (SEE) and coefficient of determination (R 2). The major findings were (1) differences between 5C, 4C and 3C models utilising the same body volume (BV) and total body water (TBW) estimates are negligible (CE ≤ 0·2 %; SEE < 0·5 %; TE ≤ 0·5 %; R 2 1·00; 95 % limits of agreement (LOA) ≤ 0·9 %); (2) moderate errors from alternate TBW or BV estimates in multi-component models were observed (CE ≤ 1·3 %; SEE ≤ 2·1 %; TE ≤ 2·2 %; R 2 ≥ 0·95; 95 % LOA ≤ 4·2 %); (3) small differences between alternate DXA (i.e. tissue v. region) and ADP (i.e. Siri v. Brozek equations) estimates were observed, and both techniques generally performed well (CE < 3·0 %; SEE ≤ 2·3 %; TE ≤ 3·6 %; R 2 ≥ 0·88; 95 % LOA ≤ 4·8 %); (4) bioimpedance technologies performed well but exhibited larger individual-level errors (CE < 1·0 %; SEE ≤ 3·1 %; TE ≤ 3·3 %; R 2 ≥ 0·94; 95 % LOA ≤ 6·2 %) and (5) anthropometric equations generally performed poorly (CE 0·6– 5·7 %; SEE ≤ 5·1 %; TE ≤ 7·4 %; R 2 ≥ 0·67; 95 % LOA ≤ 10·6 %). Collectively, the data presented in this manuscript can aid researchers and clinicians in selecting an appropriate body composition assessment method and understanding the associated errors when compared with a reference multi-component model.
Beneficial Effect of Chloroquine and Amodiaquine on Type 1 Diabetic Tubulopathy by Attenuating Mitochondrial Nox4 and Endoplasmic Reticulum Stress

Background Oxidative stress induced by chronic hyperglycemia is recognized as a significant mechanistic contributor to the development of diabetic kidney disease (DKD). Nonphagocytic nicotinamide adenine dinucleotide phosphate oxidase 4 (Nox4) is a major source of reactive oxygen species (ROS) in many cell types and in the kidney tissue of diabetic animals. We designed this study to explore the therapeutic potential of chloroquine (CQ) and amodiaquine (AQ) for inhibiting mitochondrial Nox4 and diabetic tubular injury. Methods Human renal proximal tubular epithelial cells (hRPTCs) were cultured in high-glucose media (30 mM D-glucose), and diabetes was induced with streptozotocin (STZ, 50 mg/kg i.p. for 5 days) in male C57BL/6J mice. CQ and AQ were administered to the mice via intraperitoneal injection for 14 weeks. Results CQ and AQ inhibited mitochondrial Nox4 and increased mitochondrial mass in hRPTCs under high-glucose conditions. Reduced mitochondrial ROS production after treatment with the drugs resulted in decreased endoplasmic reticulum (ER) stress, suppressed inflammatory protein expression and reduced cell apoptosis in hRPTCs under high-glucose conditions. Notably, CQ and AQ treatment diminished Nox4 activation and ER stress in the kidneys of STZ-induced diabetic mice. In addition, we observed attenuated inflammatory protein expression and albuminuria in STZ-induced diabetic mice after CQ and AQ treatment. Conclusion We substantiated the protective actions of CQ and AQ in diabetic tubulopathy associated with reduced mitochondrial Nox4 activation and ER stress alleviation. Further studies exploring the roles of mitochondrial Nox4 in the pathogenesis of DKD could suggest new therapeutic targets for patients with DKD.
BayesSuites: An Open Web Framework for Visualization of Massive Bayesian Networks

BayesSuites 1 is the ﬁrst web framework for learning, visualizing, and interpreting Bayesian networks that can scale to tens of thousands of nodes while providing fast and friendly user experience. BayesSuites solves the problems of scalability, extensibility and interpretability that massive networks bring by separating backend calculations from the frontend interface and using specialized learning algorithms for massive networks. We demonstrate the tool by learning and visualizing a genome-wide gene regulatory network from human brain data with 20,708 nodes.
Selective Studies on Delia antique(Meigen)to 4 Host Plants

Explored the onion fly(Delia antique(Meigen))adult oviposition selection in field cage and pot experiments and larval feeding preferences through indoor experiments.The results showed that the highest onion fly population occurred in onion,and the next population was in garlic and scallion,the lowest occurred in leeks through field cage experiments.The results of oviposition preference in pot experiments indicated the same trend as the field cage experiments.The lay eggs reached the most amount at onion,the lowest at leeks.The most favorite plant of the 1st larvae was onion,the next was scallion and the least were garlic and leek.The 3rd instars larvae showed the same preference as the 1st larvae.In a word,the most favorite host plant of onion fly was onion,the next was scallion and garlic,the least was leek.Moreover,we found that the oviposition selection of onion fly was the important factor in its population occurrence.So trapping and killing adult flies have applicable value in controlling onion maggot.
Statement of Research Interests

I develop secure systems that prevent advanced cybersecurity threats targeting hardware vulnerabilities. To that end, my research interests lie at the intersection of cryptography, computer architecture, and digital hardware design. Trusted computing in hardware is fundamental to information security practices. The basis of security guarantees in digital systems is essentially a set of cryptographic operations executing in a hardware root of trust. Advanced cyberattacks therefore deliberately target hardware layer vulnerabilities, especially in the context of security-critical Cyber-Physical Systems (CPS) and Internet-of-Things (IoT) applications—these attacks are difficult to detect and are much harder to thwart from the higher abstraction levels of the system. My research analyzes such vulnerabilities of hardware implementations of cyber-infrastructure. To provide practical security solutions that can be deployed in real-world settings, the systems I develop focus on implementation (side-channel) security, hardware/software efficiency, and end-to-end system demonstration. I ultimately aim to design tools that can quantify a provable security level for a given threat model and enable automated trade-offs for developers between a desired level of security, performance, and cost.
Physical stream quality measured by drones and image analysis versus the traditional manual method

ABSTRACT Information on the physical and ecological state of streams along with an overview of the need for maintenance is traditionally a time-consuming manual field task with subsequent limitations in area coverage. Here we propose a novel approach to stream monitoring and management using a low-cost Unmanned Aerial Vehicle (UAV) platform to collect data comparable to that from traditional monitoring schemes. This technology provides high-resolution imagery while being easy to implement at a low cost along with providing data that represent the stream in both fine-scale and at landscape scale. The results show a significant correlation between results obtained by the two methods, with the largest difference in DFI values being 10, but in many cases being <5. The UAV-method is especially strong in supporting geographical measurements of stream width and course along with certain stream parameters such as physical variation, water flow and gravel coverage. The results indicate that UAV mapping of streams is a feasible alternative or support to the traditional mapping of certain open stream types with the possibility of covering more area with the same time-use. GRAPHICAL ABSTRACT
The TGF-β/SMAD Signaling Pathway As a Mediator of NK Cell Dysfunction and Immune Evasion in Myelodysplastic Syndrome

Myelodysplastic syndrome (MDS) is a spectrum of clonal hematopoietic disorders affecting the myeloid lineage, characterized by ineffective hematopoiesis and dysplastic features. In about a third of patients, MDS transforms to secondary AML, and for this subgroup the overall survival is dismal. Immune responses against MDS have the potential to prevent disease progression; however, immune evasion mechanisms pose a formidable barrier. In fact, NK cells from MDS patients show significant impairment in their effector function but the mechanism underlying this immune dysfunction is not well understood. Although a multiplicity of mechanisms contribute to NK cell immune evasion, two of the most important mechanisms are down-regulation of activating receptors and the production of inhibitory cytokines such as transforming growth factor β1 (TGF-β), a broadly immunosuppressive cytokine that renders NK cells unable to kill tumor cells. We hypothesized that the MDS microenvironment evades NK cell immune surveillance through a mechanism involving TGF-β, and that this immune dysfunction can be reversed by agents that interfere with this inhibitory pathway. Thus, we isolated NK cells from the peripheral blood of MDS patients (n=16) and compared them to the NK cells from healthy donors (n=10). We observed that NK cells from high-risk MDS patients are dysfunctional, produce significantly less cytokines IFNg (p We next investigated whether targeted inhibition of TGF-β can protect NK cells from TGF-β-mediated dysfunction, using two different approaches. First, we tested the role of a TGFβR1 kinase inhibitor, Galunisertib, currently in clinical trials for MDS. The addition of Galunisertib to cocultures of healthy NK cells and myeloid blasts prevented NK cell dysfunction and blast-induced SMAD2/3 phosphorylation. For the second approach, we tested if TGF-βR2 knockout by CRISPR-CAS9 gene editing can render them resistant to the suppressive effect of TGF-β. When co-cultured with 50ng/ml of recombinant TGF-β or myeloid blasts for 48 hrs, TGF-βR2 KO NK cells retained their ability to mediate a strong effector function. In vivo experiments to assess the in vivo activity of TGF-βR2 KO NK cells in a xenograft model of myeloid leukemia are underway. Together, these data support an important role for the TGF-β/SMAD signaling pathway as a mediator of NK cell dysfunction and hence immune evasion in MDS, and support strategies to target the TGF-β/SMAD signaling axis for next-generation NK cell therapies in MDS. Disclosures Kantarjian: Bristol-Meyers Squibb: Research Funding; Novartis: Research Funding; Pfizer: Research Funding; ARIAD: Research Funding; Delta-Fly Pharma: Research Funding; Amgen: Research Funding.