Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalidation of an ELISA for Detection of a New Clinical Entity: Leishmania donovani-Induced Cutaneous Leishmaniasis

Human leishmaniasis which is considered a neglected tropical parasitic disease presents in three main clinical forms (i.e., cutaneous leishmaniasis (CL), mucocutaneous leishmaniasis (MCL), and visceral leishmaniasis (VL)) that are mainly determined by its causative species. Leishmania donovani, the most virulent and visceralizing parasite, is increasingly reported to cause CL in many countries in the world. Although CL is generally not considered to evoke a humoral immune response except for a nonrobust and a variable response in minority of cases, VL is associated with a clear strong humoral response. However, humoral response in L. donovani-induced CL has not been well evaluated before. A suitable serology-based assay is an essential primary step in such a study. An indirect enzyme-linked immunosorbent assay (ELISA) based on Leishmania promastigote crude antigen (Ag) was designed and optimized in order to utilize in further serological studies on this new clinical entity. Optimization included quantification of crude Ag, checkerboard titration method for determination of optimal concentrations for coating Ag, human sera and secondary antibody (Ab) with suitable coating buffer, blocking buffer, and incubating temperatures. The selected coating buffer was 0.02 M phosphate buffer, pH 6.8, and the blocking buffer was 2% fetal bovine serum with 0.01 M phosphate-buffered saline. At least 1 μg of crude Ag was required for coating the ELISA plate, while 1 : 1000 serum was used as primary Ab. The optimized concentration of secondary Ab was 1 : 64000 which might be altered according to manufacturer recommendations. The assay specificity was pre-evaluated using sera (n = 20 from each category) from confirmed CL patients and controls (other skin diseases which mimic CL, other systemic diseases that mimic VL, nonendemic healthy controls, and endemic healthy controls). This procedure described an optimization procedure of an ELISA technique for detection of anti-Leishmania antibodies in patients with L. donovani caused CL.
Characterizing and classifying neuroendocrine neoplasms through microRNA sequencing and data mining

Abstract Neuroendocrine neoplasms (NENs) are clinically diverse and incompletely characterized cancers that are challenging to classify. MicroRNAs (miRNAs) are small regulatory RNAs that can be used to classify cancers. Recently, a morphology-based classification framework for evaluating NENs from different anatomical sites was proposed by experts, with the requirement of improved molecular data integration. Here, we compiled 378 miRNA expression profiles to examine NEN classification through comprehensive miRNA profiling and data mining. Following data preprocessing, our final study cohort included 221 NEN and 114 non-NEN samples, representing 15 NEN pathological types and 5 site-matched non-NEN control groups. Unsupervised hierarchical clustering of miRNA expression profiles clearly separated NENs from non-NENs. Comparative analyses showed that miR-375 and miR-7 expression is substantially higher in NEN cases than non-NEN controls. Correlation analyses showed that NENs from diverse anatomical sites have convergent miRNA expression programs, likely reflecting morphological and functional similarities. Using machine learning approaches, we identified 17 miRNAs to discriminate 15 NEN pathological types and subsequently constructed a multilayer classifier, correctly identifying 217 (98%) of 221 samples and overturning one histological diagnosis. Through our research, we have identified common and type-specific miRNA tissue markers and constructed an accurate miRNA-based classifier, advancing our understanding of NEN diversity.
Universal Decoding for Asynchronous Slepian-Wolf Encoding

We consider the problem of (almost) lossless source coding of two correlated memoryless sources using separate encoders and a joint decoder, that is, Slepian-Wolf (S-W) coding. In our setting, the encoding and decoding are asynchronous, i.e., there is a certain relative delay between the two sources. Neither the source parameters nor the relative delay are known to the encoders and the decoder. Since we assume that both encoders implement standard random binning, which does not require such knowledge anyway, the focus of this work is on the decoder. Our main contribution is in proposing a universal decoder, that independent of the unknown source parameters and the relative delay, and at the same time, is asymptotically as good as the optimal maximum a posteriori probability (MAP) decoder in the sense of the random coding error exponent achieved. Consequently, the achievable rate region is also the same as if the source parameters and the delay were known to the decoder.
Construction of SARS-CoV-2 Virus-Like Particles by Mammalian Expression System

Virus-like particle (VLP) is a self-assembled nanostructure incorporating key viral structural proteins. VLP resembles molecular and morphological features of authentic viruses but is non-infectious and non-replicating due to lack of genetic materials. Successful applications of VLP has been shown in vaccinological and virological research. As an accessibly safe and relevant substitute of naturally pathogenic viruses, the construction of SARS-CoV-2 VLPs is much in demand in the ongoing fight against 2019 Coronavirus disease (COVID-19) pandemics. In the current study, using mammalian expression system, which is advantageous in maintaining correct protein glycosylation patterns, we efficiently constructed SARS-CoV-2 VLPs. We showed that among four SARS-CoV-2 structural proteins, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs. Moreover, the corona-like structure presented in SARS-CoV-2 VLPs from Vero E6 cells is more stable and unified, as compared to those from HEK-293T cells. Our data demonstrate that SARS-CoV-2 VLPs possess molecular and morphological properties of native virion particles, which endow such VLPs with a promising vaccine candidate and a powerful tool for the research of SARS-CoV-2.
The Need of Analysis on the Assessment Model of Speaking Ability Based on Information Technology

The method used in this research was Research and Development (R&D) method. R&D research is conducted through three main stages: (1) preliminary study, (2) model development, and (3) model effectiveness test. Preliminary study of assessment model development of students’ speaking ability based on information technology involves observation and questionnaire analysis. The respondents of this research were lecturer of speaking ability subject and students of Indonesian Language and Literature Education Study Program. The results of the observation and analysis of the respondents showed that (1) 85.55% stated that assessment condition of speaking competence test is currently still using manual way; (2) manual assessment has many weaknesses, and it still does not fulfill assessment principles completely; (3) 86.66% respondents expected more innovative assessment model, which is the assessment utilizing information technology; (4) the result of assessment model facilitates assessment process and the result is objective; (5) the respondents suggested the researchers to develop assessment model utilizing information technology. To fulfill their demand and suggestion, the researchers develop an assessment model which is based on information technology. The assessment model is in the form of software of assessment system that can be accessed on website. Users can access through www.mutiaraberisi. com.
Strategies for Optimizing Growth in Children With Chronic Kidney Disease

Growth failure is a hallmark in children with chronic kidney disease (CKD). Therefore, early diagnosis and adequate management of growth failure is of utmost importance in these patients. The risk of severe growth retardation is the higher the younger the child is, which places an additional burden on patients and their families and hampers the psychosocial integration of these children. Careful monitoring of growth, and effective interventions are mandatory to prevent and treat growth failure in children with CKD at all ages and all stages of kidney failure. Early intervention is critical, as all therapeutic interventions are much more effective if they are started prior to the initiation of dialysis. Prevention and treatment of growth failure focuses on: (i) preservation of renal function, e.g., normalization of blood pressure and proteinuria by use of inhibitors of the renin-angiotensin aldosterone system, (ii) adequate energy intake, including tube feeding or gastrostomy in case of persisting malnutrition, (iii) substitution of water and electrolytes, especially in children with renal malformation, (iv) correction of metabolic acidosis, (v) control of parathyroid hormone levels within the CKD-dependent target range, (vi) use of recombinant human growth hormone in cases of persistent growth failure, and, (vii) early/preemptive kidney transplantation using steroid-minimizing immunosuppressive protocols in children with end-stage CKD. This review discusses these measures based on recent guidelines.
Trans-ethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals shared but also ethnicity-specific disease associations

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD, and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such a delineation could not be made due to tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a trans-ethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9,272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40,691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analysed the physico-chemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we identified consistent associations across different ethnicities but also identified population-specific signals. We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids such. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins.
Early clinical factors predicting the development of critical disease in Japanese patients with COVID‐19: A single‐center, retrospective, observational study

The factors predicting the progression of coronavirus disease‐2019 (COVID‐19) from mild to moderate to critical are unclear. We retrospectively evaluated risk factors for disease progression in Japanese patients with COVID‐19. Seventy‐four patients with laboratory‐confirmed COVID‐19 were hospitalized in our hospital between February 20, 2020, and June 10, 2020. We excluded asymptomatic, non‐Japanese, and pediatric patients. We divided patients into the stable group and the progression group (PG; requiring mechanical ventilation). We compared the clinical factors. We established the cutoff values (COVs) for significantly different factors via receiver operating characteristic curve analysis and identified risk factors by univariate regression. We enrolled 57 patients with COVID‐19 (median age 52 years, 56.1% male). The median time from symptom onset to admission was 8 days. Seven patients developed critical disease (PG: 12.2%), two (3.5%) of whom died; 50 had stable disease. Univariate logistic analysis identified an elevated lactate dehydrogenase (LDH) level (COV: 309 U/l), a decreased estimated glomerular filtration rate (eGFR; COV: 68 ml/min), lymphocytopenia (COV: 980/μl), and statin use as significantly associated with disease progression. However, in the Cox proportional hazards analysis, lymphocytopenia at admission was not significant. We identified three candidate risk factors for progression to critical COVID‐19 in adult Japanese patients: statin use, elevated LDH level, and decreased eGFR.
Why Did Memetics Fail? Comparative Case Study1

Although the theory of memetics appeared highly promising at the beginning, it is no longer considered a scientific theory among contemporary evolutionary scholars. This study aims to compare the genealogy of memetics with the historically more successful gene-culture coevolution theory. This comparison is made in order to determine the constraints that emerged during the internal development of the memetics theory that could bias memeticists to work on the ontology of meme units as opposed to hypotheses testing, which was adopted by the gene-culture scholars. I trace this problem back to the diachronic development of memetics to its origin in the gene-centered anti-group-selectionist argument of George C. Williams and Richard Dawkins. The strict adoption of this argument predisposed memeticists with the a priori idea that there is no evolution without discrete units of selection, which in turn, made them dependent on the principal separation of biological and memetic fitness. This separation thus prevented memeticists from accepting an adaptationist view of culture which, on the contrary, allowed gene-culture theorists to attract more scientists to test the hypotheses, creating the historical success of the gene-culture coevolution theory.
The Multiple Dimensions of Multiple Determination

Multiple determination is the epistemic strategy of establishing the same result by means of multiple, independent procedures. It is an important strategy praised by both philosophers of science and practicing scientists. Despite the heavy appeal to multiple determination, little analysis has been provided regarding the specific grounds upon which its epistemic virtues rest. This article distinguishes between the various dimensions of multiple determination and shows how they can be used to evaluate the epistemic force of the strategy in particular cases. Distinguishing between the various dimensions helps to resolve the disagreements regarding the relevance and epistemic import of multiple determination for scientific research. It also suggests a fruitful mode of interaction between the philosophy of science and (historical) accounts of scientific practice.
Can neutrophil/lymphocyte ratio be used as an indicator of inflammation in patients with hyperthyroidism?

Background In our study, we aimed to evaluate changes in the neutrophil and lymphocyte series and investigate whether the neutrophil/lymphocyte ratio (NLR) is indicative of inflammations in patients with hyperthyroidism. Methods A total of 161 patients were enrolled, 121 of which had hyperthyroidism (71 Graves' Disease (GD) and 50 non-Graves hyperthyroidism (NGH) patients) and 40 of which were control group members. Retrospectively, patients' neutrophil and lymphocyte counts were taken, and the NLR was calculated. Results While the number of neutrophils was significantly lower in the GD group (p = 0.003), there was no significant difference between the NGH and the control group. In the GD group, NLR values were significantly lower than the other two groups (median 1.39 for GD, median 1.84 for NGH and median 1.83 for the control group, p < 0.001). Only three patients in the GD group had neutropenia. There was also a significant negative correlation between free T3 and neutrophil count and NLR in hyperthyroid patients (r = -0.28, p = 0.001 and r = -0.34, p < 0.001, respectively). Conclusions In our study, we found that NLR did not in crease in hyperthyroid patients and that this ratio decreased due to the decrease in neutrophil levels in GD. We thus concluded that NLR is not a suitable indicator of hyperthyroidism.
Influences of forest type and disturbance on reproduction of the brushtail possum (Trichosurus vulpecula)

Abstract The effects of forest type and disturbance on specific reproductive traits are unknown for many forest-dwelling mammals. We assessed whether differences in forest type and disturbance influenced key reproductive traits of an arboreal marsupial, the common brushtail possum (Trichosurus vulpecula), in Tasmania, Australia. Trapping was conducted in spring–summer and autumn–winter during 2007–2008 at 6 dry Eucalyptus forest sites (3 regenerating and 3 relatively undisturbed) in southeast Tasmania and 4 wet Eucalyptus forest sites (2 regenerating and 2 relatively undisturbed) in the northeast. We aged pouch young and assessed the body condition of back young. We milked females captured during the late stage of lactation and compared the nutritional composition of milk among sites. Births occurred slightly earlier at the northern sites than at those in the south. Female body mass and offspring body condition and survival were similar across sites. Milk composition also was similar across sites, but possums in dry, undisturbed forest, primarily at 1 site, produced milk with significantly higher fat content; however, we found no evidence of a difference in body condition or survival of young that could be attributed to a difference in milk quality. Although forest type and disturbance influence demography and breeding frequency in the brushtail possum populations we studied, these population-level differences are not linked to variations in the reproductive traits examined here. We conclude that the brushtail possum is a physiologically resilient species, and the ability of individual females to reproduce successfully is relatively insensitive to forest type or habitat disturbance.
Calcium and Cholecalciferol Levels in Late-Phase Laying Hens: Effects on Productive Traits, Egg Quality, Blood Biochemistry, and Immune Responses

Productive traits and immunity in laying hens decrease sharply during the late phase of laying due to aging, which negatively affects the metabolism and hormonal status of the animals. The influence of Ca levels (3.5, 4.0, and 4.5%) and/or cholecalciferol [Vitamin D3 (VD3)] supplementation (800-, 1,000-, and 1,200-IU/kg diet or as total of 3,800, 4,000, and 4,200 IC VD3) on performance, egg quality, blood biochemistry, and immunity of brown egg layers was investigated. Three hundred and sixty H&N Brown egg layers (60 weeks old) were allocated at random into nine nutritional treatments of five replications (cages) of eight hens each. The control diet in this experiment contained a 3.5% Ca level with 800 IU VD3. The addition of VD3 at 1,000 and 1,200 IU to 3.5 and 4% Ca diets significantly (P ≤ 0.05) increased the rate of laying, egg mass, and feed conversion ratio (FCR) compared to the control diet on 3.5% and 800 U of VD3. Besides this, the addition of VD3 at 800 and 1,200 IU to 3.5% Ca level diets enhanced the Haugh unit score. Similar results were observed in eggshell quality measurements and tibia ash. Increasing the Ca concentration from 3.5 to 4 and 4.5% and increasing VD3 levels from 800 to 1,000 or 1,200 IU significantly and similarly increased serum total protein and globulin. In addition, VD3 at 1,000 IU increased serum albumin, compared to 800 IU. Increasing Ca level increased IgA, and 4 and 4.5% Ca levels similarly increased IgG and α-2 globulin compared to the 3.5% Ca diet. VD3 addition at 1,200 IU to the 4% Ca diet significantly increased γ-globulin compared to 1,000 IU, but decreased β-globulin. Increasing the Ca level to 4% significantly reduced serum triglycerides, and the very low-density lipoprotein and the triglyceride/high-density lipoprotein ratio were both decreased with 4 and 4.5% Ca level diets. Increasing the Ca level caused a stepwise increase in catalase, which was markedly increased with VD3 supplementation at 1,200 IU. Plasma estrogen was increased considerably with VD3 supplementation at 3.5% Ca, but parathyroid hormone levels were not affected. In conclusion, increasing Ca levels in the diet of laying hens to 4% during the late production phase could be a useful tool to improve laying performance, eggshell quality, Haugh unit score, and physiological and immunological status. Besides, VD3 at a 1,000 IU/kg diet to 3.5% Ca improved performance of hens fed 3.5% Ca, showing that the potential impact of VD3 depends on Ca concentrations.
The Protective Effect and Mechanism of Dexmedetomidine on Diabetic Peripheral Neuropathy in Rats

Objective To investigate the role of dexmedetomidine (DEX) in the inhibition of diabetic peripheral neuropathy (DPN) and the protection in the nerve damage. Methods Eighty male Sprague-Dawley (SD) rats were randomly allocated to four groups: the control group (C group), DPN model group (DPN group), DEX-treated group (DEX group), and the yohimbine treated group (YOH group). DPN was induced by intraperitoneal administration of streptozocin (STZ) (35 mg/kg). The body weights, blood glucose level, mechanical withdrawal threshold (MWT), thermal withdrawal latency (TWL), the motor, and sensory nerve conduction velocities (MNCV and SNCV) of sciatic nerve were measured. Then the sciatic nerve was isolated for H&E staining and immunohistochemical staining. The oxidative stress makers such as malondialdehyde (MDA), superoxide-dismutase (SOD), and glutathione peroxidase (GSH-Px) and apoptosis related cytokines such as Bax, Bcl-2, and caspase-3 were estimated. Results There was no significant difference of the blood glucose and body weight among the DPN group, DEX group, and YOH group. H&E staining showed that DEX treatment can ameliorate the damage of sciatic nerve cells. In the DPN group, MWT, TWL, MNCV, and SNCV were significantly reduced compared with the C group (P < 0.05). In DEX group rats, MWT, TWL, MNCV, and SNCV were increased significantly (P < 0.05) compared with the DPN group and YOH group rats. Lower SOD and GSH-Px, and higher MDA were found in the DPN group compared with the C group (P < 0.01), and DEX treatment restored SOD, GSH-px, and MDA activity significantly (P < 0.01). The expression levels of Bax and caspase-3 were increased, while that of Bcl-2 was decreased significantly in the DPN group compared with the C group (P < 0.05). In the DEX group, the expression levels of Bax and caspase-3 were decreased significantly (P < 0.05), while that of Bcl-2 was increased significantly (P < 0.05) compared with the DPN group and the YOH group. Conclusion The results of this study demonstrated that DEX has the inhibitory and protective effects on DPN of rats. This may be associated with its antioxidative and anti-apoptosis responses.