Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing heat stress tolerance and genetic diversity among exotic and Indian wheat genotypes using simple sequence repeats and agro-physiological traits

Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.
Surprisingly modern Latest Cretaceous–earliest Paleocene woods of India

Background and approach – The Deccan Intertrappean Beds of Central India contain a diverse assemblage of fossil plants, including petrified woods from 15 localities. These beds are dated at c. 67–64 Ma, i.e. latest Cretaceous–earliest Paleocene and span the K-Pg boundary, a significant time in angiosperm history. At this time, the Indian tectonic plate was halfway on its journey from Gondwana to its collision with Asia, and relatively close to the equator. We provide descriptions in IAWA Hardwood List codes for 47 species of Deccan fossil woods, based on our examination of thin sections of these woods, mostly holotypes that are housed at the Birbal Sahni Institute of Palaeobotany, Lucknow, India. An appendix lists all validly published Deccan wood species of which we are aware, including 52 that we were not able to examine. Main results – The Deccan fossil woods described herein include the oldest known occurrences of some orders, families or genera viz. Lamiales (Lamiaceae), Achariaceae (Hydnocarpus-like wood), Anacardiaceae, Simaroubaceae (Ailanthus-like and Simarouba-like woods), subfamily Leeoideae (Vitaceae), subfamily Myrtoideae (Myrtaceae), subfamily Planchoideae (Lecythidaceae), tribe Castilleae (Moraceae), tribes Grewioideae and Sterculioideae (Malvaceae). These first fossil records are discussed with reference to other macrofossil and pollen records of the same or related clades. They complement recent work on the oldest known Olea and Connaraceae also documented by Deccan woods.For the Deccan woods we examined, we could confirm the earlier taxonomic assignment at least down to order or family level for 29 taxa. Ordinal level affinities are ambiguous for eight of the taxa. In two cases, we revised the taxonomic assignment to other families; for another eight, the original assignment was found to be incorrect, but we are unable to suggest alternative affinities. Evolutionary implications – Only 3% of all Deccan woods have scalariform perforations and the incidences of so-called specialized features in the Baileyan sense are high, so these woods have a remarkably “modern” aspect. This is anomalous in comparison with contemporaneous fossil woods from higher paleolatitudes, and seemingly they are more “derived” than the recent flora. In these respects, the Deccan woods constitute a unique assemblage. The low incidence of scalariform perforations suggests xeric conditions, while – in contrast – the low incidence of distinct growth ring boundaries suggests an aseasonal everwet climate. It is speculated that convergent xylem specialization, especially the selection for simple perforations, was enhanced by the climatic conditions found at low paleolatitudes with high temperatures as would characterize the Deccan Intertrappean Beds at the K-Pg boundary.
Evaluation of potential prebiotics: a review

ABSTRACT Prebiotics are any undigested food ingredients that are selectively fermented and allow for specific changes in the gut microbiota, thus improving the hosts’ health. In order to assess the potential of a food component to be considered as a prebiotic ingredient, several in vitro and in vivo experimentations need to be performed to provide scientific substantiation. In vitro studies are widely used because they are faster, cheaper, and more ethical compared to in vivo studies. However, in vitro studies faced difficulties in simulating the highly complex physiological and physiochemical events occurring in animal and human digestive tracts. Therefore, it is recommended that the results of in vitro studies be justified with in vivo experimentations to support their specific methodologies. Devised standard procedures for the evaluation and validation of prebiotic ingredients will boost confidence among the scientific community, approval of regulators, and acceptance from consumers on prebiotics and functional food science.
Single-Molecule Studies Of tRNA Dynamics During Ongoing Translation

The pre-translocation complex of the ribosome can undergo spontaneous fluctuations of mRNA and tRNAs between classical and hybrid states, and occupation of the hybrid tRNA positions has been proposed to precede translocation. The classic and hybrid state tRNA positions been extensively characterized when the ribosome is stalled along the messenger RNA by either the absence or the delayed addition of elongation factor G (EF-G), or by the presence of antibiotics or GTP analogs that block translocation. Surprisingly, during multiple ongoing elongation cycles when both EF-G and ternary complexes are present, we found that tRNA positions in PRE complex ribosome do not fluctuate. Instead, they adopt a stationary intermediate structure between the stalled classical and hybrid tRNA positions, as indicated by single molecule fluorescence resonance energy transfer (FRET) between adjacent tRNAs and between A-site tRNA and ribosomal protein L11. These results indicate that EF-G promotes the formation of an intermediate structure during ongoing translation. smFRET experiments using labeled EF-G at those concentrations requires zero-mode waveguides (ZMWs), arrays of nanoscale holes in a thin metal film that confine the observation volume to reduce prohibitive background fluorescence. However, the need for specialized nanofabrication equipment has precluded their widespread adoption by the biochemical community. In contrast, nanosphere lithography uses the selfassembly of polystyrene beads into a hexagonal array, forming a natural lithographic mask for the deposition of metallic posts in the interstices between beads, followed by a different metal cladding around the posts and dissolution of the posts to leave a well array. The cross-sectional size of those interstices (and thus subsequent posts and wells) can be finely tuned by fusing the beads at the polystyrene glass transition temperature. That bead lattice serves as a template for creating sub-wavelength ZMWs with little specialized equipment and at a low cost, enabling wide-scale adoption. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Bioengineering First Advisor Yale E. Goldman Subject Categories Biochemistry | Biomedical | Biophysics This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/2357 SINGLE-MOLECULE STUDIES OF tRNA DYNAMICS DURING ONGOING TRANSLATION Ryan Jamiolkowski A DISSERTATION in Bioengineering Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2016 Supervisor of Dissertation _________________________________________ Dr. Yale E. Goldman, Professor of Physiology Graduate Group Chairperson __________________________________________ Dr. Jason Burdick, Professor of Bioengineering Dissertation Committee: Dr. Andrew Tsourkas, Professor of Bioengineering Dr. Robert Doms, Professor of Pathology and Laboratory Medicine Dr. Arjun Raj, Professor of Bioengineering
The comparison of blood characteristics in low- and high-altitude chickens

Abstract Tibetan chicken (TC) is a unique chicken breed that has inhabited the Tibetan Plateau for thousands of years and has adapted to the harsh environment of an altitude of over greater than 4000 m. The changes in blood characteristics that occur in high-altitude rearing of TCs are unknown. To obtain a deeper insight into the blood characteristics of chickens in low and high altitudes, we focussed on four chicken populations to compare the variations among them. In the present study, we found significant differences in white blood cell (WBC) count, red blood cell (RBC) count and haematocrit (HCT) values between TCs and other chicken populations. When TCs were reared at low altitude, there was a significant (p < .05) decrease in the WBC, RBC and HCT values compared with the TCs reared at high altitude; however, whether the mean corpuscular volume (MCV) value is related to oxygen transport and hypoxia adaptation requires further study. It is likely that haemoglobin (HGB), mean corpuscular haemoglobin (MCH) and MCH concentration (MCHC) values are decrease at high-altitude hypoxic environments. Therefore, the increase in WBC, RBC and HCT values may be the common haematological mechanism for TCs to adapt to high-altitude hypoxia. These research results provide the scientific basis and theory to explain how TCs are able to adapt to high-altitude hypoxia.
A 3D digitizing tool to determine fruit quality distribution within the canopy

The "Slender Spindle", one of the most used training systems for apple, was compared with the "Bi-axis", an innovative training system, to determine their effect on fruit quality and fruit distribution within the canopy on 'Gala' cultivar. Two levels of crop loads were also introduced to observe their effects through chemical and manual thinning. Fruit position in the canopy was monitored during summer using different software to draw in 3D the tree architecture. Also, fruits were monitored during the growing season for their growth and maturation. At the end of the season, fruits were harvested, graded and analyzed for their quality traits. Fruit position had a strong influence on fruit quality. The fruits in the layers were significantly different. In the upper part of the tree, fruits had a higher percentage of over color and bigger fruit size compared to the middle and the lower part of the canopy. No significant differences were found between the two training systems. Crop load influenced fruit quality in both training systems in the same way on fruit size and over color. The lowest crop load treatment had a higher percentage of over color and bigger fruit size compared to the higher crop load.
Evaluation of growth rates and resistance to nematodes of Deccani and Bannur lambs and their crosses with Garole

Sheep rearing is a traditional occupation of about 85 000 shepherd families on the Deccan plateau in the Maharashtra State of India. They rear Deccani (D) sheep which usually bear only single lambs. Prolificacy is an important trait for the efficiency of meat producing sheep. It was decided to evaluate and utilize Indian sheep genetic resources with a view to improving the efficiency of sheep production on the Deccan plateau. A crossbreeding experiment was conducted over 4 years, using rams of the D, Bannur (B) and Garole (G) breeds and D and B ewes with the aim of developing recommendations for the appropriate breed combination of a likely composite. It was found that crossing with G reduces live weight and growth rates significantly compared with D but lambs sired by G rams were more resistant to naturally acquired gastro-intestinal nematode infections and to artificial challenge with Haemonchus contortus than those sired by D or B rams. The G breed, being from a humid environment is, however, not adapted to the semi-arid Deccan plateau. The higher productivity (in terms of weight of lamb weaned) of twin-bearing ewes compared with those bearing singles was evident even in extensive rearing conditions. The finding of increased resistance to gastro-intestinal nematodes in the G breed, which also carries a major gene for prolificacy, highlights the potential for inclusion of G in a composite breed. Negative effects on growth and survival from inclusion of the Garole need to be carefully managed.
Assessment of the Contribution of Antagonistic Secondary Metabolites to the Antifungal and Biocontrol Activities of Pseudomonas fluorescens NBC275

An understanding of the contribution of secondary metabolites (SMs) to the antagonistic and biocontrol activities of bacterial biocontrol agents serves to improve biocontrol potential of the strain. In this study, to evaluate the contribution of each SM produced by Pseudomonas fluorescens NBC275 (Pf275) to its antifungal and biocontrol activity, we combined in silico analysis of the genome with our previous study of transposon (Tn) mutants. Thirteen Tn mutants, which belonged to 6 biosynthetic gene clusters (BGCs) of a total 14 BGCs predicted by the antiSMASH tool were identified by the reduction of antifungal activity. The biocontrol performance of Pf275 was significantly dependent on 2,4-diacetylphloroglucinol and pyoverdine. The clusters that encode for arylpolyene and an unidentified small linear lipopeptide influenced antifungal and biocontrol activities. To our knowledge, our study identified the contribution of SMs, such as a small linear lipopeptide and arylpolyene, to biocontrol efficacy for the first time.
Hypothyroidism and Nonalcoholic Fatty Liver Disease: Pathophysiological Associations and Therapeutic Implications

Abstract Nonalcoholic fatty liver disease (NAFLD) is a complex clinical entity which can be secondary to many other diseases including hypothyroidism, characterized by lowering of thyroid hormones and increased thyroid stimulating hormone (TSH). A lot of emerging data published recently advocates the hypothesis that hypothyroid induced NAFLD could be a separate clinical entity, even suggesting possible treatment options for NAFLD involving substitution therapy for hypothyroidism along with lifestyle modifications. In addition, a whole new field of research is focused on thyromimetics in NAFLD/NASH treatment, currently in phase 3 clinical trials. In this critical review we summarized epidemiological and pathophysiological evidence linking these two clinical entities and described specific treatment options with the accent on promising new agents in NAFLD treatment, specifically thyroid hormone receptor (THR) agonist and its metabolites.
Localization and restaging of carcinoma prostate by 68Gallium prostate-specific membrane antigen positron emission tomography computed tomography in patients with biochemical recurrence

Introduction: Radical prostatectomy (RP) and radical radiotherapy (RT) are well established primary curative options for localized prostate cancer. Despite technical improvements, prostate-specific antigen (PSA)-recurrence after RP and RT is a common clinical scenario. We aimed to assess the role of 68Gallium (68Ga) prostate-specific membrane antigen positron emission tomography computed tomography (PSMA PET/CT) in patients with biochemical recurrence of prostate cancer after RP or RT for the detection and localization recurrent and metastatic disease. Materials and Methods: We ambispectively (70 retrospective and 100 prospective) analyzed the data of men with biochemical recurrence post-RP and post-RT who were evaluated by 68Ga PSMA PET/CT at our institute. We aimed to assess the relationship between serum PSA levels and the probability of having a positive scan in patients with recurrent prostate cancer. Results: The study included 170 men, all had adenocarcinoma of the prostate, 124/170 had previous RP and 46/170 had prior RT. The median serum PSA in the RP group was 1.8 ng/ml and 5.2 ng/ml in the RT group. In the post-RP cohort, the detection rate of 68Ga PSMA PET/CT was 39.3% for PSA 0.2 to <0.5 ng/ml, 47.3% for PSA 0.5 to <1 ng/ml, 68.4% for PSA 1 to <2 ng/ml and 93.1% for PSA ≥2 ng/ml. In the post-RT group, the detection rate was 88.8% for PSA 2 to <4 ng/ml and 100% for PSA ≥4 ng/ml. Conclusions: 68Ga PSMA PET/CT provides a novel imaging modality for the detection of prostate cancer recurrence and metastases at low posttreatment PSA levels, which may help in directing appropriate salvage treatments.
Prevalence and Associated Risk Factors of Human Intestinal Protozoan Parasitic Infections in Ethiopia: A Systematic Review and Meta-Analysis

Background Human intestinal protozoan parasitic infections (HIPPIs) are a series of public health problems in developing countries like Ethiopia. The overall prevalence of HIPPIs in Ethiopia is not known. Therefore, this systematic review and meta-analysis study is aimed at determining the overall prevalence of HIPPIs in Ethiopia. Methods Articles written in English were searched from online public databases. Searching terms used were “prevalence,” “intestinal protozoan parasite,” “associated factors,” and “Ethiopia. ” We used Stata version 14 for meta-analysis and Cochran's Q test statistics and the I2 test for heterogeneity. Result A total of 286 articles were reviewed, but only 45 of them fulfilled the inclusion criteria. The pooled prevalence of HIPPIs in Ethiopia was 25.01% (95% CI: 20.08%-29.95%) where Entamoeba histolytica/dispar is the most prevalent (14.09%, 95% CI: 11.03%-17.14%) followed by Giardia lamblia (10.03%, 95% CI: 7.69%-12.38%) and Cryptosporidium spp. (5.93%, 95% CI: 2.95%-8.91%). This meta-analysis showed that family size (OR: 3.7, 95% CI: 1.45-5.85), source of drinking water (OR: 3.33, 95% CI: 1.30-5.36), open field defecation (OR: 2.91, 95% CI: 1.60-4.21), handwashing habit (OR: 2.82, 95% CI: 2.01-3.63), playing with soil (OR: 2.15, 95% CI: 1.01-3.29), the habit of eating raw vegetables (OR: 1.77, 95% CI: 1.03-2.51), and fingernail trimming (OR: 1.70, 95% CI: 0.89-2.25) were strongly associated with the HIPPIs in Ethiopia. High heterogeneity on the prevalence of HIPPIs was observed among studies within and among regions (I2 > 99% and P ≤ 0.01). Conclusion The prevalence of HIPPIs was significantly high among the Ethiopian population. Family size, source of drinking water, open field defecation, handwashing habit, the habit of eating raw vegetables, and fingernail trimming habits were significantly associated with HIPPIs.
Healthcare Engineering: A Lean Management Approach

This work tries to answer the following question: can healthcare be engineered using lean management tools? Lean is known to achieve successful results when implemented in the manufacturing sector. Typical results are operational cost reduction, cycle time reduction, and higher customer satisfaction. The service sector, however, has seen mixed results. For the last two decades, educators and healthcare professionals are trying to implement lean tools in healthcare. Some reported success and many did not, for variety of reasons. In this paper, we search the literature and reveal the special nature of healthcare services, success factors, and barriers facing implementation of lean in healthcare. We then conduct a survey of 18 elite Jordanian hospitals to study the case holistically. Statistical analysis of the survey results confirmed some of what the literature revealed; organizational leadership seems to be the most dominant factor, followed by knowledge of employees about lean, training, and patient satisfaction (customer focus). Another important finding, not captured by the literature, is that lean implementation success depends on educating physicians about continuous improvement and lean and ensuring they are part of the improvement team. Based on the revealed enablers and obstacles, we created a full lean implementation framework. This framework was then used along with selected engineering tools to implement lean in a major hospital successfully. Implementation results showed 60% of reduction in cycle time, 80% reduction in operational cost, and many other benefits.
Incomplete Trifascicular Block and Mobitz Type II Atrioventricular Block in COVID-19

A 74-year-old female with a history of diabetes presented with chest pain and shortness of breath for two days. She was hypoxic to an oxygen saturation of 60% in the emergency department, requiring bilevel positive airway pressure (BiPAP) to maintain saturations. Chest X-ray demonstrated bilateral hazy opacities suspicious for viral pneumonia. Coronavirus disease 2019 (COVID-19) was confirmed. Right bundle branch block (RBBB) with left anterior fascicular block was noted on admission electrocardiogram (ECG). Cardiac enzymes and brain natriuretic peptide levels were within normal limits. After noting frequent pauses on telemetry, a repeat ECG was performed that demonstrated RBBB with left posterior fascicular block as well as second-degree atrioventricular block (Mobitz type II). Transcutaneous pacing pads were placed, and atropine was placed at the bedside. Cardiac enzymes remained negative. Interleukin-6 levels were elevated at 159 pg/mL. Hydroxychloroquine was deferred due to the patient’s arrhythmia and prolonged QTc. Tocilizumab was deferred due to the patient’s age. The patient’s oxygen requirements and mental status continued to worsen. She continued to desaturate despite maximal BiPAP therapy and eventually died. Cardiac involvement in COVID-19, whether caused primarily by the virus, secondary to its clinical sequelae, or even due to its treatment, cannot be ignored. Further high-quality research is needed to clarify the cardiac pathophysiology. Thorough cardiac exams with electrocardiographic correlation should be performed on all patients with COVID-19. Clinicians should not hesitate to consult cardiovascular services in the event of abnormality.
Endothelial, pericyte and tumor cell expression in glioblastoma identifies fibroblast activation protein (FAP) as an excellent target for immunotherapy

Targeted immunotherapies such as chimeric antigen receptor (CAR)‐T cells are emerging as attractive treatment options for glioblastoma, but rely on identification of a suitable tumor antigen. We validated a new target antigen for glioblastoma, fibroblast activation protein (FAP), by undertaking a detailed expression study of human samples.
EFFECT OF INTERACTION BETWEEN BIOCONTROL FUNGUS TRICHODERMA HARZIANUM AND MYCORHIZAL FUNGUS GLOMUS MOSSAE IN FUSARIUM WILT DISEASE ON SOME PEPPER CULTIVARS

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