Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Molecular Variance and Population Structure of Sesame (Sesamum indicumL.) Genotypes Using Simple Sequence Repeat Markers

Sesame ( Sesamum indicum L.) is an important oilseed crop grown in tropical and subtropical areas. The objective of this study was to investigate the genetic relationships among 129 sesame landraces and cultivars using simple sequence repeat (SSR) markers. Out of 70 SSRs, 23 were found to be informative and produced 157 alleles. The number of alleles per locus ranged from 3 - 14, whereas polymorphic information content ranged from 0.33 - 0.86. A distance-based phylogenetic analysis revealed two major and six minor clusters. The population structure analysis using a Bayesian model-based program in STRUCTURE 2.3. 4 divided 129 sesame accessions into three major populations ( K = 3). Based on pairwise comparison estimates, Pop1 was observed to be genetically close to Pop2 with F ST value of 0.15, while Pop2 and Pop3 were genetically closest with F ST value of 0.08. Analysis of molecular variance revealed a high percentage of variability among individuals within populations (85.84%) than among the populations (14.16%). Similarly, a high variance was observed among the individuals within the country of origins (90.45%) than between the countries of origins. The grouping of genotypes in clusters was not related to their geographic origin indicating considerable gene flow among sesame genotypes across the selected geographic regions. The SSR markers used in the present study were able to distinguish closely linked sesame genotypes, thereby showing their usefulness in assessing the potentially important source of genetic variation. These markers can be used for future sesame varietal classification, conservation, and other breeding purposes.
Several Factors Associated With Nitrogen Balance In Elderly Patients

Background: Nitrogen balance is the method used to assess the protein adequacy. A negative nitrogen balance means that the body suffers from protein energy malnutrition. Objective: To determine the risk factors that associated with nitrogen balance in the elderly patients who were inpatient in IRNA Internal Medicine Dr. Soetomo General Hospital Surabaya. Methods: The experimental design of the research used was analytic observational with the cross-sectional design. The study was conducted of 50 elderly patients. Risk factors measured were protein intake using food recall and nitrogen excretion that expressed in Urea Nitrogen Urine (gr / 24 h). The nitrogen balance was derived from the difference between nitrogen intake and nitrogen excretion in 24 hours. Bivariate data analysis using Chi square or exact fisher test, while multivariate data analysis using logistic regression test. Results: In bivariate analysis, risk factors significantly associated with negative nitrogen balance were decreased renal function (LFG <90 ml / min / 1.73 m2), prolonged bed rest> 7 days and malnutrition. Other risk factors not significantly associated with negative nitrogen balance were diabetes mellitus, random blood sugar> 180 mg / dl, hypoalbumin and CRP> 6 mg / dl. In multivariate analysis showed the decrease of renal function and duration of bed rest > 7 days was significant. Conclusion : The decreased renal function and bed rest for more than 7 days was a risk factor for protein malnutrition in elderly patients.
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

The composition of the cell nucleus is highly heterogeneous, with different constituents forming complex interactomes. However, the global patterns of these interwoven heterogeneous interactomes remain poorly understood. Here we focus on two different interactomes, chromatin interaction network and gene regulatory network, as a proof-of-principle, to identify heterogeneous interactome modules (HIMs) in the nucleus. Each HIM represents a cluster of gene loci that are in spatial contact more frequently than expected and that are regulated by the same group of transcription factor proteins. We develop a new algorithm MOCHI to facilitate the discovery of HIMs based on network motif clustering in heterogeneous interactomes. By applying MOCHI to five different cell types, we found that HIMs have strong spatial preference within the nucleus and exhibit distinct functional properties. Through integrative analysis, this work demonstrates the utility of MOCHI to identify HIMs, which may provide new perspectives on 3D genome organization and function.
Factors that affect the ruminal microbial composition and methods to determine microbial protein yield

Microbial protein synthesized in the rumen is a major contributor of metabolizable protein. Thus, accurate estimation of microbial protein is essential in ruminant nutrition. The objective of this review is to describe the microbial composition, major factors affecting its yield and methods to estimate microbial protein flow to the intestine. The use of novel molecular techniques to elucidate the ruminal microbiome and improve methods for estimating microbial protein are discussed. Bacteria, protozoa, fungi and archaea compose the ruminal microbiome. Main factors affecting microbial protein synthesis are availability of carbohydrates, ruminally degradable protein, dietary fat, and ruminal pH. Major microbial markers used to estimate microbial protein synthesis are total purines, diaminopimelic acid and labeled nitrogen; in addition, DNA through real-time PCR is being tested for the estimation of bacterial, protozoal and yeast protein separately. The main difficulty in the estimation of microbial protein flow is obtaining representative microbial pellets from the rumen, which are used as reference to establish the ratio of marker/nitrogen. Detailed phylogenetic analysis using High-throughput DNA sequencing has recently revealed drastic taxonomic differences between fluid-associated bacteria and bacteria from whole intestinal digesta contents. For example, ruminal fluid contains less Fibrobacteres and Proteobacteria , but more Firmicutes compared to whole intestinal digesta. This demonstrates the need of developing effective bacterial collection procedures for obtaining representative ruminal microbial reference pellets to prevent bias on the estimation of the contribution of microbial protein to the intestinal supply of metabolizable protein.
Programmable Ring Oscillator PUF Based on Switch Matrix

Configurable ring oscillator (CRO) physical unclonable functions (PUFs) which can improve the uniqueness and reliability of conventional RO PUFs have been widely studied. Especially, the multiplier, XOR gate and tristate inverter based CRO PUFs can improve the uniqueness and reliability. However the efficiency is remain at the same level when compared with the conventional RO PUFs. In this paper, a programmable RO PUF (PRO PUF), which can be programmed to change the structure of a typical RO PUF, is proposed. The proposed PRO PUF design is implemented based on the switch matrix of an FPGA and can be programmed as a chained RO PUF or a random looped RO PUF. The proposed PRO PUF is implemented on Xilinx Spartan 6 FPGAs. Experimental results demonstrate that the proposed PRO PUF design has good uniqueness and reliability metrics as well as a high hardware efficiency.
Characterization of the atmospheric effects on the transmission of thermal radiation

Atmospheric scattering plays a crucial rule in degrading the performance of electrooptical imaging systems operating in the visible and infra-red spectral bands, and hence limits the quality of the acquired images, either through reduction of contrast or increase of image blur. The exact nature of light scattering by atmospheric media is highly complex and depends on the types, orientations, sizes and distributions of particles constituting these media, as well as wavelengths, polarization states and directions of the propagating radiation. Here we follow the common approach for solving imaging and propagation problems by treating the propagating light through atmospheric media as composed of two main components: a direct (unscattered), and a scattered component. In this work we developed a detailed model of the effects of absorption and scattering by haze and fog atmospheric aerosols on the optical radiation propagating from the object plane to an imaging system, based on the classical theory of EM scattering. This detailed model is then used to compute the average point spread function (PSF) of an imaging system which properly accounts for the effects of the diffraction, scattering, and the appropriate optical power level of both the direct and the scattered radiation arriving at the pupil of the imaging system. Also, the calculated PSF, properly weighted for the energy contributions of the direct and scattered components is used, in combination with a radiometric model, to estimate the average number of the direct and scattered photons detected at the sensor plane, which are then used to calculate the image spectrum signalto-noise ratio (SNR) in the visible near infra-red (NIR) and mid infra-red (MIR) spectral
«Kids Do Well If They Can» – Guiding Principles in Health Promoting Work in Kindergartens and Schools

In the programme Health Promoting Kindergartens and Schools, we work across various educational contexts, and our goal is to facilitate for good mental health where individuals thrive and can develop their potential. The background for this programme was increased mental health challenges among young people. We believe it is important to have a common set of values to create an environment that embraces difference and promotes a positive development. We have developed a set of guiding principles which are as follows: 1) There are no difficult children, only children who are going through difficulties. This principle is inspired by Ross Green’s saying «Kids do well if they can», and it expresses a professional responsibility to act according to what children and young people express through words or action. 2) We see development as a possibility, meaning that it is always possible to influence a situation. 3) We develop solutions together, meaning that children and young people are supported to be actors in their own lives depending on age and matureness. 4) We know that we are all part of the context, meaning that we must be conscious of our own attitudes and understandings when meeting with others. To ensure that the different participants in the programme work according to the same principles, we gathered different professionals from the education and health sectors, and used a method called Dialogue Cafe to discuss the four principles. In this presentation, we will elaborate on this process, and how the four guiding principles were understood.
Human CtIP forms a tetrameric dumbbell-shaped particle which binds and bridges complex DNA end structures for double-strand break repair

CtIP is involved in the resection of double-stranded DNA breaks during the S and G2 phases of the cell cycle for repair by homologous recombination. Acting in concert with the MRN complex, it plays a particularly important role in handling complex DNA end structures by localised nucleolytic processing of DNA termini in preparation for longer range resection. Here we show that human CtIP is a tetrameric protein adopting a dumbbell architecture in which DNA binding domains are connected by long coiled-coils. The protein complex binds two short DNA duplexes with high affinity and bridges DNA molecules in trans. DNA binding is potentiated by dephosphorylation and is not specific for DNA end structures per se. However, the affinity for linear DNA molecules is increased if the DNA terminates with more complex structures including forked ssDNA overhangs and model nucleoprotein conjugates. This work provides a biochemical and structural basis for the function of CtIP at complex DNA breaks.
Prey-predator interactions derived from energy metabolism: Reconsideration of ontogenetic metabolic scaling

Faculty of Fisheries, Nagasaki University Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies Center for Ecological Research, Kyoto University (JSPS Research fellow) Laboratory of Plant Ecology, Department of Environmental Science, Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University Plant Ecology Research Division, Forestry and Forest Products Research Institute Fishery Research Laboratory, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University
Zn and Cd hyperaccumulating characteristics of Picris divaricata Vant. Int J Environ Pollut

A field investigation and a pot experiment were conducted to study the Zn and Cd accumulation in Picris divaricata Vant. Under natural conditions, the average Zn and Cd concentrations in shoot of P. divaricata were 5911 and 246 µg g -1 (DW), with the maxima of 18,339 and 585 µg g -1 , respectively. Grown on a mixed soil for three months, P. divaricata accumulated up to 15,183 µg g -1 Zn and 364 µg g -1 Cd in shoot with translocation factors of Zn and Cd all larger than one. Thus, P. divaricata could be identified as a new Zn and Cd hyperaccumulator found in China.
The area under the precision‐recall curve as a performance metric for rare binary events

Species distribution models are used to study biogeographic patterns and guide decision‐making. The variable quality of these models makes it critical to assess whether a model's outputs are suitable for the intended use, but commonly used evaluation approaches are inappropriate for many ecological contexts. In particular, unrealistically high performance assessments have been associated with models for rare species and predictions over large geographic extents. We evaluated the area under the precision‐recall curve (AUC‐PR) as a performance metric for rare binary events, focusing on the assessment of species distribution models. Precision is the probability that a species is present given a predicted presence, while recall (more commonly called sensitivity) is the probability the model predicts presence in locations where the species has been observed. We simulated species at three levels of prevalence, compared AUC‐PR and the area under the receiver operating characteristic curve (AUC‐ROC) when the geographic extent of predictions was increased and assessed how well each metric reflected a model's utility to guide surveys for new populations. AUC‐PR was robust to species rarity and, unlike AUC‐ROC, not affected by an increasing geographic extent. The major advantages of AUC‐PR arise because it does not incorporate correctly predicted absences and is therefore less prone to exaggerate model performance for unbalanced datasets. AUC‐PR and precision were useful indicators of a model's utility for guiding surveys. We show that AUC‐PR has important advantages for evaluating models of rare species, and its benefits in the context of unbalanced binary responses will make it applicable for other ecological studies. By not considering the true negative quadrant of the confusion matrix, AUC‐PR ameliorates issues that arise when the geographic extent is increased beyond the species’ range or when a large number of background points are used when absence information is unavailable. However, no single metric captures all aspects of performance nor provides an absolute index that can be compared across datasets. Our results indicate AUC‐PR and precision can provide useful and intuitive metrics for evaluating a model's utility for guiding sampling, and can complement other metrics to help delineate a model's appropriate use.
Early gonadal differentiation in the Mexican snook Centropomus poeyi (Centropomidae, Perciformes, Teleostei) suggests protandric hermaphroditism

ABSTRACT This study describes for the first time the early gonadal morphogenesis and raises the possibility of occurrence of protandric hermaphroditism in the Mexican snook (Centropomus poeyi). To achieve this, histological analysis of early gonadal differentiation was performed in 105 juvenile specimens ranging from 136 to 367 days post-hatching (dph). The early gonadal differentiation of the Mexican snook started at 178–213 dph and was completed at 355–367 dph. Active spermatogenesis was observed at 355–367 dph, once the compartmentalization of testis in germinal and interstitial compartments was accomplished. Our study demonstrates that in the Mexican snook, early gonadal differentiation is directed to produce 100% males, implying protandric hermaphroditism and showed the presence of a long-lasting period of gonadal differentiation, which makes this species highly sensitive to environmental cues.
Economics of Boro Rice Production in Rangpur District of Bangladesh: Comparative Assessment of Urea Super Granule and Traditional Urea Application

Corresponding Author: Aurup Ratan Dhar Department of Agricultural Economics, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh Email: aurup971@gmail.com Abstract: The study was examined the profitability of Boro rice production using Urea Super Granule (USG) and traditional urea in Rangpur district of Bangladesh. 60 farmers were selected randomly for the present study. The cultivation of Boro rice was profitable from the viewpoint of the farmers. Per hectare net return for USG user and traditional urea user was Tk. 40264.4 and Tk. 26740.2, respectively. Benefit cost ratio for USG user and traditional urea user was estimated at 1.5 and 1.3, respectively. BCR was higher for USG user because they were efficient producer. Power tiller cost, seed/seedling cost, TSP cost, MoP cost, cowdung cost and irrigation cost; and human labor cost, seed/seedling cost, urea cost, MoP cost, cowdung cost and irrigation cost had significant impact on gross return from Boro rice production for USG and traditional urea user, respectively. Age of farmer, price of USG, soil nutrient availability and extension contact had significant impact on farmers’ preference for using USG in Boro rice production. The price of fertilizer should be regulated strictly by the government and extension programs should be arranged in order to motivate farmers for adopting USG use in Boro rice production.
Enhancing antibody-dependent cell-mediated cytotoxicity: a strategy for improving antibody-based immunotherapy

ABSTRACT The targeting of surface antigens expressed on tumor cells by monoclonal antibodies (mAbs) has revolutionized cancer therapeutics. One mechanism of action of antibody-based immunotherapy is the activation of immune effector cells to mediate antibody-dependent cell-mediated cytotoxicity (ADCC). This review will summarize the process of ADCC, its important role in the efficacy of mAb therapy, how to measure it, and finally future strategies for antibody design that can take advantage of it to improve clinical performance.
A multimodal approach to identify clinically relevant parameters to monitor disease progression in a preclinical model of neuropediatric disease

While research has accelerated the development of new treatments for pediatric neurodegenerative disorders, the ability to demonstrate the long-term efficacy of these therapies has been hindered by the lack of convincing, noninvasive methods for tracking disease progression both in animal models and in human clinical trials. Here, we unveil a new translational platform for tracking disease progression in an animal model of a pediatric neurodegenerative disorder, CLN6-Batten disease. Instead of looking at a handful of parameters or a single “needle in a haystack”, we embrace the idea that disease progression, in mice and patients alike, is a diverse phenomenon best characterized by a combination of relevant biomarkers. Thus, we employed a multi-modal quantitative approach where 144 parameters were longitudinally monitored to allow for individual variability. We use a range of noninvasive neuroimaging modalities and kinematic gait analysis, all methods that parallel those commonly used in the clinic, followed by a powerful statistical platform to identify key progressive anatomical and metabolic changes that correlate strongly with the progression of pathological and behavioral deficits. This innovative, highly sensitive platform can be used as a powerful tool for preclinical studies on neurodegenerative diseases, and provides proof-of-principle for use as a potentially translatable tool for clinicians in the future. One Sentence Summary Principal component analysis identifies a set of clinically relevant parameters able to measure progression of Batten disease in a mouse model.
The Effectiveness of Dry Needling on Dimensions and Elastic Modulus of the Nasolabial Fold due to Aging Process: An Uncontrolled before-after Clinical Trial Study

Introduction: Biomechanical properties of the skin change with pathological conditions and aging process. Nasolabial fold (NLF) is a degenerative manifestation of the skin tissue, which facilitates biomechanical properties measurement due to its quantifiable scales. The aim of this study was to evaluate the effectiveness of dry needling on decreasing NLF dimensions and improving NLF skin biomechanical properties. Materials and methods: 11 women aged between 35-55 years with NLF class between 2-2.5 were selected for study, and received 7 sessions of dry needling treatment. Another group of young women between 20-30 years considered as control group and received no treatment. NLF depth and area, epidermis and dermis thickness, and young modulus of NLF skin were analyzed with high resolution ultrasonography and a custom-made forceguage. For reliability of sonographic data the interclass correlation coefficient, and for between and within group comparisons, independent and paired t tests were used, respectively. Results: NLF depth and area decreased significantly (P < 0.001). Moreover, epidermis and dermis thickness and young modulus increased significantly (P < 0.001). Conclusion: Dry needling induced decrease in depth and area, and improved biomechanical properties of the NLF, without any side effect.
Anti-elastase, Antioxidant, Total phenolic and Total Flavonoid Content of Macassar Kernels (Rhus javanica L) from Pananjung Pangandaran Nature Tourism Park- Indonesia

Background : Phytochemicals are present as important substances in natural resources and therefore, have aided in invention of the anti-oxidant, and anti-elastase properties of polyphenol compounds present in Indonesian herbs such as Macassar Kernels ( Rhus javanica L. Objective: This research aimed to investigate anti-elastase, and antioxidant properties. Methods: Ethanolic extract of Rhus Leaves (RL), Rhus Stem (RS), Rhus Greenish Fruit (RGF), and Rhus Blackish-grey Fruit (RBF) were prepared individually by solvent extraction method. Anti-elastase activity was carried out with elastase from porcine pancreas. For quantitative phytochemical screening, DPPH radical scavenging assay, Ferric Reducing Antioxidant Power Assay (FRAP), Total Phenolic Content (TPC), Total Flavonoid Content (TFC) of Rhus javanica were estimated. Result: RS showed highest anti-elastase activity (45.30% ± 0.087), compared with RL (12.30% ± 0.004), and there were no activities in RGF and RBF. In DPPH assay, RS had lowest activity (IC 50 561.05 μg/ml), compared with RBF (IC 50 239.28 μg/ml), RGF (IC 50 189.3I μg/ml), and RL (IC 50 157.81 μg/ml). RS also has lowest FRAP activity (% inhibition = 26.60% ± 0.002), and TPC value (28.50 ± 0.03 mgGAE/g dry weight). Conclusion: Test extracts showed anti-aging properties in different mechanisms. RS possessed the highest anti-elastase activity but had the weakest antioxidant activity.