Miracle-dz/UniFAR-FTUs huggingface dataset:
Latent Tuberculosis Infection: Patho-Biology and Treatment

Tuberculosis continues to be an epidemic disease worldwide especially in the developing countries. One of the main reasons behind the continuation of this epidemic is latent tuberculosis infection. Globally, 2 – 3 billion people have latent TB infection. Prevention of reactivation TB is now considered as one of the important strategies of TB prevention and is one of the main pillars for the WHO “ End TB Strategy. ” Biostatistical modeling has shown that protecting 8% of persons with latent tuberculosis every year can bring down the global incidence rate by 14 times by 2050 as compared to that in 2013 without any other intervention. One of the most effective strategies recommended by WHO has been Isoniazid preventive therapy for 6 – 9 months. Chemoprophylaxis for LTBI can prevent 60 – 90% of reactivation TB. Isoniazid preventive therapy is considered safe; however, it can occasionally result in significant adverse effects like hepatitis and rarely mortality. In conclusion, chemoprophylaxis of LTBI can be considered an important intervention being done to curb the epidemic of TB especially in high-risk group and reduce the morbidity and mortality associated with active TB disease.
Effects of oral glucose on exercise thermoregulation in men after water immersion

To test the hypothesis elevated blood glucose would attenuate the rise in exercise rectal temperature, six men age 35 plus or minus S.D. 7 years participated in each of three trials by 4-hr water immersion to the neck: (1) 2.0 g/kg body wt of oral glucose (33.8 percent wt./vol.) was consumed followed by 80 min controlled rest (Glu/Rest), and 70 min horizontal supine cycle exercise at 62.8 percent plus or minus S.E. 0.5 percent (1.97 plus or minus 0.02 L/min) of peak O2 uptake followed by 10 min recovery (2) with (Glu/Ex) and (3) without prior flucose (No Glu/Ex). Blood samples were taken at -25, 0, 15, 45, and 68 min of exercise and after plus 10 min of recovery for measurement of hemoglobin, hematocrit, and blood glucose. Both mean skin (T sub sk) (from six sites) and rectal temperatures (T sub re) were monitored continuously. Sweat rate was measured by resistanc hygrometry. The mean of delta PV for the exercise trials was -12.2 plus or minus 2.1 percent. Mean blood glucose for the Glu/Ex trial was higher than that of the No Glu/Ex trial was (108.4 equal or minus 3.9 and 85.6 plus or minus 1.6 mg/dl, respectively, P less than 0.05. At the end of exercise T(sub sk) for the Glu/Ex trial was lower than for No Glu/Ex(32.0 plus or minus 0.3 and 32.4 equals or minus 0.2 C, respectively, P less than 0.05); T(sub re) for the Glu/Ex trial was lower than for No Glu/Es (38.22 plus or minus 0.17 and 38.60 plus or minus 0.11 C, respectively, P less than 0.05); and forearm sweat rate for the Glu/Ex trial (0.34 plus or minus 0.04 and 0.43 plus or minus g/sq cm, respectively, P less than 0.05). These data suggest that elevation of blood glucose prior to horizontal exercise following hypohydration attenuates the increase in body temperature without altering heat production or exercise hypovolemia.
Relationship between patient-perceived quality of nurse caring attitudes and behaviours and quality of life of haemodialysis patients in Switzerland

Background: Chronic kidney disease (CKD) is a fast-growing cause of morbidity and mortality worldwide. Patients suffering from CKD almost always develop end-stage renal disease (ESRD) that is often treated with haemodialysis (HD). In this context, the quality of the nurse-patient relationship (NPR) plays a major role in supporting the quality of life (QoL) of HD patients. This study examined the relationship between quality of nurse behaviours and attitudes as perceived by HD patients and QoL of these patients.Methods: The study used a cross-sectional correlational design. The sample consisted of 140 patients recruited in 10 HD units in French-speaking Switzerland. The Caring Nurse-Patient Interaction Scale (CNPI-70) was used to assess the NPR, and the French version of the WHOQOL-Bref was used to evaluate different dimensions of QoL. Random-intercept linear regressions adjusted for sociodemographic characteristics were used to study the relationship between patient-perceived quality of nurse caring attitudes and behaviours and patient QoL.Results: Patients reported a high frequency of caring attitudes and behaviours from their attending nurses, except relative to the dimension of spirituality. All the dimensions of patient QoL were positively influenced by the caring factor composing the CNPI-70. In particular, nurse attention to patient dignity when providing support for basic human needs seemed to be a major factor in patient QoL.Conclusions: Quality of NPR is essential to improving patient QoL. Interventions need to be developed to support quality of NPR.
A regression approach to estimate the relative roles of pollen- versus seed-mediated gene flow under an isolation by distance model

Abstract In the present work, a new estimator to be known as rIBD is proposed. The proposed estimator indirectly quantifies the relative role of gene flow mediated by pollen in relation to the gene flow mediated by seeds in hermaphrodite angiosperm species when an isolation by distance model is assumed. The proposed estimator complements the well-known estimator proposed by Ennos, which is appropriate for studies under the island model. In the present work, the proposed rIBD index was used to analyze microsatellite data from uni- and biparentally inherited genomes generated by simulations, as well as for the analysis of an empirical data set obtained from public databases of forest tree species. The differences in median values of the proposed rIBD index for simulated data using the Stepping Stone Model and Truncated Pareto Distribution Model coincided with the magnitude expected in terms of differences between levels of pollen and seed dispersion previously established in the simulations. In empirical data, the proposed rIBD index shows lower levels of gene flow by seed versus gene flow by pollen, the ratio between them being three times lower than the ratio obtained by the Ennos index estimated under the island model. From the analyses carried out, it is feasible to consider the rIBD index as a suitable estimator of the role of gene flow by seeds in relation to gene flow by pollen under isolation by distance.
Understanding Performance Concerns in the API Documentation of Data Science Libraries

The development of efficient data science applications is often impeded by unbearably long execution time and rapid RAM exhaustion. Since API documentation is the primary information source for troubleshooting, we investigate how performance concerns are documented in popular data science libraries. Our quantitative results reveal the prevalence of data science APIs that are documented in performance-related context and the infrequent maintenance activities on such documentation. Our qualitative analyses further reveal that crowd documentation like Stack Overflow and GitHub are highly complementary to official documentation in terms of the API coverage, the knowledge distribution, as well as the specific information conveyed through performance-related content. Data science practitioners could benefit from our findings by learning a more targeted search strategy for resolving performance issues. Researchers can be more assured of the advantages of integrating both the official and the crowd documentation to achieve a holistic view on the performance concerns in data science development.
Genetic and Phylogenetic Diversity of Escherichia coli Strains Collected From Fecal Specimens of Patients Admitted to Zabol Hospitals

Introduction: Escherichia coli is one of the most prevalent bacterial species which cause gastrointestinal and digestive tract infections in humans and livestock. This study examined genotypic diversity of the E. coli isolates taken from fecal specimens in Zabol using random amplification of polymorphic DNA (RAPD) method and phylogenetic background.Materials and Methods: In this study, 100 isolates were collected from human samples and identified by the common biochemical tests. The isolates were categorized into four main phylogenetic groups including group A (28 isolates), group B1 (7 isolates), group B2 (48 isolates), and group D (17 isolates). Two primers (H1 & H2) were used to study the genetic variation of E. coli and the electrophoresis band pattern was analyzed by the NTSYS.Results: The analysis of the difference in isolates using the RAPD technique showed a genetic similarity between 14% and 100%. Conclusion: The phylogenetic groups B2 and A were more frequent in fecal isolates. In addition, the number of isolates related to phylogenetic groups B1 and D was significantly lower than that of the other groups.
The Maximum Length Record of the Blackspot Seabream (Pagellus bogaraveo Brünnich, 1768) for the Entire Aegean Sea and Turkish Territorial Waters

Received : 11/05/2020 Accepted : 29/06/2020 The maximum length, weight, and age information of organisms in an ecosystem, moreover, the first records of migrated exotic species are essential in terms of the basis for the studies on population dynamics, stock assessment, and biological activities. Therefore, the recording of such data may be necessary for scientific databases and new related studies. The Blackspot seabream (Red seabream Pagellus bogaraveo), which belongs to the Sparidae family, is an important seafood which is marketed fresh and frozen around the Mediterranean and the Aegean seas. Nowadays, this species has high prices depending on market demands in domestic markets as a result of overfishing and is also cultured in northern Spain. It is classified as “Near Threatened Species” in the red list due to its decreasing population trend by the IUCN. A single specimen of the Blackspot seabream with 30.7 cm in total length and 390.00 g in total weight, which was angled in the Saros Bay with a handline by a fisherman on February 08, 2019, was obtained from a fishmonger in Çanakkale. Even though there are bigger individuals in the North-east Atlantic probably depending on polar and/or deep-sea gigantism, the mentioned measurement is the proven maximum total length of this species for the Aegean Sea up to the time.
Isolation and identification of natural product inhibitors of Plx2A, a toxin from Paenibacillus larvae

ISOLATION AND IDENTIFICATION OF NATURAL PRODUCT INHIBITORS OF PLX2A, A TOXIN FROM PAENIBACILLUS LARVAE Chantal A. Wood Advisor: University of Guelph, 2018 Dr. Rod Merrill Mono-ADP-ribosyltransferase (mART) toxins are an important class of virulence factors generated by bacterial pathogens that promote many disease states in the target host. They catalyze the hydrolysis of the glycosidic bond joining nicotinamide with the N-ribose of NAD and transfer ADP-ribose to a target protein. Plx2A has recently been characterized as a mART toxin from the honey bee pathogen Paenibacillus larvae that plays a key role in American Foulbrood disease in honeybees. An HPLC-based NAD-glycohydrolase assay was developed and used to reveal several plant extracts that demonstrated inhibition of Plx2A enzymatic activity. Additionally, a library of natural product-derived compounds chosen based on structure-guided modelling was tested against Plx2A, which identified one compound with inhibitory activity. The fractionation of the most promising extracts was achieved by solid-phase extraction with the analysis of these fractions by HPLC. Plant extracts provide novel lead inhibitors against these toxins to be used as potential therapeutics.
High concordance of programmed death-ligand 1 expression with immunohistochemistry detection between antibody clones 22C3 and E1L3N in non-small cell lung cancer biopsy samples

Background The detection of programmed death-ligand 1 (PD-L1) expression can enrich for patients who respond to anti-programmed cell death 1 (PD-1)/PD-L1 therapies. Though, for most laboratories, the cost of PD-L1 22C3 pharmDx is prohibitive for widespread use, whereas the laboratory-developed test (LDT) PD-L1 E1L3N antibody clone is widely available and inexpensive. This study aims to explore the analytical performance of E1L3N on the Dako Autostainer Link-48 platform and further evaluate the concordance of E1L3N and 22C3 expression in non-small cell lung cancer (NSCLC) biopsy samples. Methods A total of 171 NSCLC biopsy samples were utilized in this study. Cases with less than 100 tumor cells were excluded. Serial sections of representative blocks were used for immunohistochemistry (IHC) staining. The staining protocol was performed according to the standard PD-L1 IHC 22C3 pharmDx package. PD-L1 staining on the tumor cell membrane was detected by immunofluorescence. Results At a 1% cutoff value, PD-L1 was positive in 46.2% of patients using clone 22C3 and 42.1% of patients using E1L3N assays. At a 50% cutoff value, PD-L1 was positive in 16.4% of patients using clone 22C3 and 15.2% of the patients using E1L3N assays. Cohen’s kappa was used to evaluate the concordance of the PD-L1 expression between clone 22C3 and E1L3N. The kappa values were 0.893 [95% confidence interval (CI): 0.826–1] at the 1% cutoff and 0.868 (95% CI: 0.764–1) at the 50% cutoff. An evaluation of the intraclass correlation coefficients (ICCs) between the antibodies was used to quantify the interassay variability for PD-L1 expression in tumor cells. ICCs showed high concordance between the two antibodies (0.955, 95% CI: 0.939–0.967). Cohen’s kappa was also used to assess the consistency of the PD-L1 evaluation between two pathologists. The kappa values were 0.941 and 0.912 at the 1% cutoff, and 0.904 and 0.909 at the 50% cutoff for clone 22C3 and E1L3N expression, respectively. Conclusions The results indicated that the clone E1L3N assay has a high concordance with 22C3. The PD-L1 clone E1L3N assay is reliable and cost-effective, and could be used as a primary screening agent for PD-L1 IHC staining in pathological laboratories, especially in a research setting.
Utilizing photonic crystal structure to design microstrip antenna with controllable dielectric constant substrate

A novel design method of microstrip patch antenna with photonic crystal substrate is proposed and analyzed. The method is different from the traditional one. Early work uses natural materials as the substrate to design microstrip patch antenna. In the work, dielectric cylinder arrays are designed based on periodic waveguide theory to realize the substrates with controllable dielectric constants. Meanwhile, applying dielectric cylinder array and microstrip antenna design theory, we designed and simulated a new type of antenna. The proposed antenna model is compared with homogeneous substrate structure antenna-based microstrip patch antenna and analyzed the radiation characteristics. The consistency of results shows that this method is feasible for antenna design. Afterwards, we fabricated a novel antenna with an equivalent dielectric constant of 2.94, which is further verify the feasibility of the method. Finally, the performance of designed antenna is analyzed with different cylinder height. The results show that the novel antenna design method maybe possess great significance to the design of high-gain miniaturized antenna.
Simulation of reactive solute transport in the critical zone: A
Lagrangian model for transient flow and preferential transport

We present a method to simulate fluid flow with reactive solute transport in structured, partially saturated soils using a Lagrangian perspective. In this context, we extend the scope of the Lagrangian Soil Water and Solute Transport Model (LAST) (Sternagel et al., 2019) by implementing vertically variable, non-linear sorption and first-order degradation processes during transport of reactive substances through a partially saturated soil matrix and macropores. For sorption, we develop an explicit mass transfer approach based on Freundlich isotherms because the common method of using a retardation factor is not applicable in the particlebased approach of LAST. The reactive transport method is tested against data of plotand field-scale irrigation experiments with the herbicides isoproturon and flufenacet at different flow conditions over various periods. Simulations with HYDRUS 1-D serve as an additional benchmark. At the plot scale, both models show equal performance at a matrix-flowdominated site, but LAST better matches indicators of preferential flow at a macropore-flow-dominated site. Furthermore, LAST successfully simulates the effects of adsorption and degradation on the breakthrough behaviour of flufenacet with preferential leaching and remobilization. The results demonstrate the feasibility of the method to simulate reactive solute transport in a Lagrangian framework and highlight the advantage of the particle-based approach and the structural macropore domain to simulate solute transport as well as to cope with preferential bypassing of topsoil and subsequent re-infiltration into the subsoil matrix.
Determination of Antioxidant Effects of Some Medicinal Plants and Investigation of their Physicochemical Characters

The objective of this study is to determine the antioxidant activity and phytochemical constituents of methanol extract of five medicinal plants. Preliminary phytochemical screening was determined using modified method of Harbone while quantitative phytochemical test was carried out using HPLC technique method of AOAC. Preliminary phytochemical screening revealed the presence of flavonoids, phenols alkaloids, tannins and saponinsin the extract of V. donniana, P. biglobosa, E. convoluvloide, F. gnaphalocarpa and S. occidentalis. Anthraquinones was present in P. biglobosa extract only. Quantitative phytochemical test revealed that E. convolvuloide extract (0.92 ± 0.10 % w/w) and (0.29 ± 0.05 % w/w) has high amount of flavonoids and phenols respectively. Alkaloids, tannins and anthraquinones were high in F. gnaphalocorpa (36.06 ± 1.17 mg/100), V. doniana (1.10 ± 0.02 mg/100) and P. biglobosa (0.09 ± 0.01 mg/ml) respectively. DPPH radical scavenging activity, ABTS radical scavenging activity, hydrogen peroxide radical scavenging activity and ferric reducing antioxidant power method was used for Antioxidant determination. The results were expressed as percentage inhibition and IC50 (where 50% concentration of the extract scavenged free radical). S. occidentalis extract (IC50: 41.80 µg/ml) and (IC50: 69.19 µg/ml) scavenged free radicals using DPPH and FRAP methods compared to other extract. F. gnaphalocarpa extract (IC50: 44.63 µg/ml) and E. convolvuloides extract (IC50: 72.77 µg/ml) scavenged free radicals using ABTS and hydrogen peroxide radical scavenging methods compared to compare to other extracts.
Critical Roles of Non-coding RNAs in Acute Lymphoblastic Leukemia

MicroRNA(miRNA)isoneof thenon-codingRNA(ncRNA)moleculeswith21-25-nucleotidelength,playinganimportantroleingene controlbytranscriptionalgeneregulation,chromatinremodeling,geneticimprinting,andtranslationinitiation. Thederegulation of ncRNAcanleadtoseveralhematopoieticmalignanciessuchasacutelymphoblasticleukemia(ALL). Thestudyaimedtodrawthe crucialfeaturesof miRNAinthepathogenesisof ALL. TheﬁndingsshowedthatmiRNAexpressionchangesinALLaretypicalandin-volveseveralsignalingpathways. ThevariationsinmiRNAgeneexpressioncanleadtotheincompleteexpressionof oncoproteinor tumorsuppressorgene(TSG). ItseemsthatncRNAsplaypivotalrolesintheALLpathogenesis. However,ncRNAsmightbeinterested as potential diagnostic and prognostic biomarkers in ALL.
Extracellular vesicles as mediators of the response to respiratory exposures

Inhaling noxious substances increases the risk of pulmonary and cardiovascular disease. This study investigated whether this is mediated by extracellular vesicles, small membrane bubbles which transfer information between cells. When exposed to noxious substances such as cigarette smoke and air pollutants, lung cells released vesicles which promoted blood coagulation. These vesicles may contribute to thrombotic events such as myocardial infarction. The antioxidant N-acetylcysteine prevented the induction of procoagulant vesicles. Measuring procoagulant vesicles in blood may be useful for predicting which exposed individuals are likely to develop cardiovascular disease and antioxidants may be used to protect this high-risk group.
A Preliminary Occurrence of Extended-Spectrum and AmpC Beta-Lactamases in Clinical Isolates of Enteropathogenic Escherichia coli in Najaf, Iraq

Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase producing enteropathogenic Escherichia coli (EPEC) have become an important clinical problem due to their resistance to multiple antibiotics. The purpose of this study was to evaluate the multi-drug resistant (MDR) and β-lactamases producing EPEC isolated from children with diarrhea. Twenty two EPEC strains were gathered from another study performed from September to November 2009. Antibiotic susceptibilities against 20 antibiotics determined by the agar disk diffusion according to the protocol recommended by Clinical and Laboratory Standards Institute guidelines (CLSI). Phenotypic confirmatory tests carried out for screening of ESBLs and AmpC β-lactamase. The isolates subjected to PCR assays with specific primers for bla-genes (blaSHV, blaTEM, blaCTX-M and blaOXA, blaPER, blaVEB and blaGES). Only 22 (3.4%) EPEC isolates recovered from clinical infections. MDR rate in EPEC was 90.9%. Phenotypic confirmatory tests showed that 13.6% and 20.0% of isolates were ESBL and AmpC β-lactamase producers, respectively. Among the EPEC isolates, percent recovery of blaSHV, blaTEM, blaCTX-M and blaOXA genes was 100%, 81.8%, 77.3% and 9.1%, respectively. Only 2 (9.1%) isolates had blaAmpC gene and none of the isolates carried blaPER, blaVEB and blaGES genes. The results of our study showed that the ESBLs were common among EPEC isolates. Such high dissemination of ESBLs is a serious problem for public health and therefore, it is necessary to seek a program for monitoring ESBLs in Najaf hospitals. This study is the first report on the presence of the bla-genes in EPEC isolates in Najaf.
From local to national metabolism: a review and a scale-up framework

ABSTRACT Research background: Countries are likely the most important subjects involved in the environmental control and response to global environmental issues, while the majority of the related metabolic analyses are focused on the metabolism at the city scale. Objective: Analyzing why and how to scale up the metabolic study from city to country. Methods: Combining quantitative analysis with a literature review socio-metabolic research, since it is an effective method to study resource and environmental issues and has been applied at different scales. Results: 1) A single city or a smaller area is hardly self-sufficient, and its sustainability and resilience needs the support of the surrounding environment; 2) At the country scale, systems exhibit a higher level of self-organization and a corresponding higher level of complexity, addressing the need for applying the metabolic theory at the national scale; 3) The emergy analysis methods show its advantages in study metabolic processes for national metabolism; 4) Input-output analysis plays an important role in and region coordination. Conclusions: The interactions among and within the scales are nested, as well as the goals and methods. Therefore, socio-metabolic research on scales differ in their priority goals, and the methods adopted must be targeted.