Miracle-dz/UniFAR-FTUs huggingface dataset:
CALCIUM REQUIREMENT IN RELATION TO MILK FEVER FOR HIGH YIELDING DAIRY COWS: A REVIEW

The purpose of this paper is to review the predisposing factors and advances in controlling principles of milk fever in high yielding dairy cows. Dietary imbalances in dairy cows can be one of fundamental cause of numerous and complicated types of health problems that are usually categorized as metabolic disorders. High producing dairy cows are among highly susceptible animal to such metabolic disorders during their transitional periods; three weeks before and after calving. In these periods, the animal struggles to maintain their calcium homeostasis; which is the most common metabolic disorder of high yielding dairy cows, due to their underlying physiological and pathological factors. Thus, those factors predisposing dairy cows to milk fever are age, stage of lactation and parity, body condition and diet. Usually, the basic principle of controlling milk fever is feeding the cows from diet constituting lower calcium and potassium contents in dry period. So that calcium mobilization from bone would be promoted, which ensures the increased metabolic processes of calcium mobilization during the transition period? Furthermore, supplementations of various anionic salts which includes magnesium sulfate, calcium sulfate, ammonium sulfate, calcium chloride, ammonium chloride and magnesium chloride are commonly used to raise blood calcium level, thus, minimizes risks of milk fever. Also, body condition management of cows during dry period is used to prevent milk fever. Finally, a recent research indicates that serotonin intravenous injections have significantly reduced the incidence of hypocalcemia in high yielding dairy cows.
Dynamic walking control of humanoid robots combining linear inverted pendulum mode with parameter optimization

To improve the robustness of biped walking, a model parameters optimization method based on policy gradient decent learning is presented. For the linear inverted pendulum mode-based model parameters optimization, firstly, select the input parameters of the inverted pendulum model and the torso attitude parameters of the robot as the correction variables and establish the correction equation. Then, using the tracking errors of center of mass (CoM) of the robot and the errors of the robot posture relative to the upright state of the body to establish the fitness function. According to the fitness function, the gain coefficients in the model parameters correction equation are optimized by using the strategy gradient learning method, and the modified gain parameters are substituted into the model parameters correction equation to obtain the correction amount. By applying the model parameters optimization strategy, the robot can quickly and in real time adjust the body posture and walking patterns under unknown disturbances, hence, the walking robustness can be enhanced. Simulation and experiments on a full-body humanoid robot NAO validate the effectiveness of the proposed method. The experiments show that the optimized model yields a more controlled, robust walk on NAO robot and on various surfaces without additional manual parameters tuning.
Short Communication: Behavioral study on Anguilla bicolor using a modified trap design at laboratory scale

Abstract. Fitri ADP, Boesono H, Kurohman F, Jayanto BB, Dewi DE, Sabdono A. 2019. Short Communication: Behavioral study on Anguilla bicolor using a modified trap design at laboratory scale. Biodiversitas 20: 2159-2165. The information on the behavioral juvenile eels Anguilla bicolor is urgently needed as basic design of selective and sustainable traps. The objectives of this study were to find out and analyze the behavioral pattern and characteristics of A. bicolor elvers in the modified and non-modified eel traps. The test organism, A. bicolor juvenile eels with 150-170 mm in length, were obtained from Segara Anakan waters, Cilcacap. The 2 trap designs, which were modifications of the 450 mm long PVC eel trap, with and without the addition of bait hole, were used in this study. All experiments were carried out in the laboratory of Fish Behavior, Diponegoro University, Semarang, Indonesia. The eel characters and response time were recorded using a handy camera that placed on top of the aquariums. The results indicated six types of A. bicolor behavior in response to the modification of eel traps. Moreover, the trap design with an additional hole on the wall, with or without bait, was proven to have no significant effect on the response time. While trap without column and bait possessed the fastest response time at which elver penetrated to the trap (p-value ≤ 0.05). Furthermore, these results indicated that A. bicolor elver gained entrance into the trap, in an attempt to take shelter.
pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks

Motivation Modern genomic research relies heavily on next-generation sequencing experiments such as ChIP-seq and ChIA-PET that generate coverage files for transcription factor binding, as well as DHS and ATAC-seq that yield coverage files for chromatin accessibility. Such files are in a bedGraph text format or a bigWig binary format. Obtaining summary statistics in a given region is a fundamental task in analyzing protein binding intensity or chromatin accessibility. However, the existing Python package for operating on coverage files is not optimized for speed. Results We developed pyBedGraph, a Python package to quickly obtain summary statistics for a given interval in a bedGraph file. When tested on 8 ChIP-seq and ATAC-seq datasets, pyBedGraph is on average 245 times faster than the existing program. Notably, pyBedGraph can look up the exact mean signal of 1 million regions in ~0.26 second on a conventional laptop. An approximate mean for 10,000 regions can be computed in ~0.0012 second with an error rate of less than 5 percent. Availability pyBedGraph is publicly available at https://github.com/TheJacksonLaboratory/pyBedGraph under the MIT license.
Interactive Three-Dimensional Image Analysis and Visualization Using Graphics Hardware

Image analysis is a process of extracting useful information from input images using various image processing techniques, such as denoising, enhancement, feature detection, and segmentation. State-of-the-art techniques employ sophisticated and time-consuming nonlinear processes to capture subtle and detailed information from images that may be overlooked by classical linear methods. In addition, with the advent of the recent advance in imaging technology, high resolution images of several hundreds gigabytes become common these days. Such recent trends in image processing require computationally expensive processes and make the interactive image analysis challenging. In this dissertation I propose novel three-dimensional nonlinear image processing algorithms and their efficient implementations on modern graphics processors for interactive image analysis, specifically targeting the geoscience and medical applications. Over the past decade, the graphics processing unit (CPU) has evolved into a powerful computing platform for high performance computation. Among many applications, image processing can be a good candidate to achieve a significant speed-up using the GPU because it is inherently a data parallel process. The main motivation of the proposed dissertation research is to accelerate time-consuming image analysis applications using inexpensive commodity CPUs. This dissertation consists of three parts. First, an interactive 3D seismic fault detection system is proposed. I have developed a structure-oriented directional anisotropic diffusion filter and a variance-based fault detection algorithm, and introduced their efficient implementations on the GPU. Second, I propose a fast parallel algorithm for weighted distance computation using a Hamilton-Jacobi framework. The proposed algorithm is based on a label-correcting scheme for scalability on single instruction multiple data (SIMD) parallel architectures. Finally, I propose a probabilistic framework for user-assisted 3D elongated structure segmentation, and show the acceleration techniques using the CPU implementation of nonrigid image registration and probability computation. A number of synthetic and real-world 3D datasets, such as seismic, CT, and DT-MRI volumes, are used to assess the validity and effectiveness of the proposed methods.
Effects of yeast culture (Saccharomyces cerevisiae) supplementation on growth performance, fecal score, and nutrient digestibility of weaning pigs

Weaning pigs often face post-weaning challenges such as diarrhea, low feed intake, and body weight (BW) loss which affects the health and economic value of weaning pigs. Interestingly, the use of yeast cultures (YCs) as feed supplements for pigs has increased markedly in recent years. This study evaluated the effects of yeast cultures (Saccharomyces cerevisiae) on the growth performance, fecal score, and nutrient digestibility of weaning pigs. A total of 50 crossed healthy weaning pigs [(Yorkshire × Landrace) × Duroc] with an average BW of 7.46 ± 1.60 kg (28 day of age) were used in a 6-week experiment. The experiment was divided into 3 phases (Phase 1, 1 2 weeks; Phase 2, 2 4 weeks; Phase 3, 4 6 weeks). Dietary treatments were as follows: 1) CON: basal diet and 2) CON + 0.50% YC. During phase 1, the average daily gain (ADG) and average daily feed intake (ADFI) were significantly increased (p < 0.05) in the weaning pigs fed YC supplementation diets compared with the weaning pigs fed the CON diet. During phase 3 as well as overall, the gain/feed ratio (G/F) was significantly increased (p < 0.05) in the YC supplementation group compared with the pigs fed the CON diet. In conclusion, the supplementation of YCs in the diet positively affected the growth performance of weaning pigs during the first two weeks after weaning.
The concentration and probabilistic health risk assessment of nitrate in Iranian drinking water: a case study of Ilam city

Abstract In this study, the concentration of nitrate in 11 drinking water points in Ilam city was investigated, and furthermore, the consumer’s probabilistic health risk was assessed. The nitrate levels in cumulative probability plot (CPD) of 50% (CEXP50) and 95% (CEXP95) were calculated as 8.12 and 16.37 mg/L, respectively, while in all samples (n = 77) were measured as significantly (ρ value) lower than 50 mg/L (the proposed reference value by the World Health Organization (WHO) as well as Iranian national standard. Considering the probabilistic health risk; Hazard Quotient 50% (HQ50) and Hazard Quotient 95% (HQ95) were measured as 0.21 and 0.4, (HQ <1), respectively. Based on acceptable daily intake dose, HQ50s for men, women, and children were 0.09, 0.07, and 0.11 while HQ95s were 0.16, 0.12, and 0.22, respectively. Therefore, the order of the Hazard Quotients (HQ50 and HQ95) based on the age group of consumers was summarized as children > men > women. The health risk assessment shows that all consumers are safe of health risk.
Endoplasmic reticulum associated degradation preserves hematopoietic stem cell quiescence and self-renewal by restricting mTOR activity

Many tissue-specific stem cells require quiescence to sustain stem cell pool and maintain lifelong tissue integrity. It remains unclear whether protein quality control is required for stem cells in quiescence when RNA content, protein synthesis and metabolic activities are significantly reduced. Here, we report that endoplasmic reticulum associated degradation (ERAD) is required to preserve the function of quiescent hematopoietic stem cells (HSC). The Sel1L/Hrd1 ERAD genes are enriched in the quiescent and inactive HSCs, and conditional knockout of Sel1L in hematopoietic tissues drives HSCs to hyper-proliferation which leads to reduced self-renewal and HSC depletion. ERAD deficiency induces a non-apoptotic ER stress and activates unfolded protein response (UPR). Furthermore, Sel1L knockout leads to mTOR activation, and mTOR inhibition rescues the HSC defects in Sel1L knockout mice. Protein quality control is, therefore, tightly regulated and actively engaged in quiescent HSCs. Sel1L/Hrd1 ERAD maintains HSC quiescence and self-renewal via restricting mTOR activity.
Zika Virus RNA Degradation In Municipal Wastewater

stable than assumed. This study was a pilot study to develop evidence for further exploration of materials and methods for detection of ZIKV RNA in wastewater. Cost-effective methods to detect ZIKV RNA in municipal wastewater such as this will be of crucial importance to better understand the burden ZIKV has on a community during epidemics due to challenges faced on detecting ZIKV infections in the clinical setting.
The complete mitogenome of Smith’s shrew (Chodsigoa smithii)

Abstract The Smith’s shrew (Chodsigoa smithii) belongs to subfamily Soricinae, which is an endemic shrew to China. In this study, we obtained the complete mitochondrial genome of the C. smithii. This mitogenome is a circular molecule with 17,108 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, one light strand replication origin (OL), one non-coding region, and with a base composition of 32.5% A, 29.3% T, 24.8% C, and 13.4% G. The nucleotide sequence data of 13 protein-coding genes of C. smithii and other 19 Soricomorpha species were used for phylogenetic analyses. Phylogenetic tree shows that Soricinae includes two major phylogenetic lineages. Chodsigoa smithii is located as a basal position in tribe Nectogalini.
Studies on yield and biochemical sub-components of latex of rubber trees (Hevea brasiliensis) with a special reference to the impact of low temperature in a non-optimal environment

This study was conducted to examine the relationship of yield with latex sub-components with a special reference to low temperature effects in five commercially popular clones (GT1, RRll 105, RR11118, PB 235, and RRIM 600) of rubber tree Hevea brasiliensis in a non-traditional area of rubbet cultivation in North-East India where low temperature prevails in winter There was a dear seasonal and clonal variation in yield The pre-winter (October to November) was the broad peak yielding period Rubber yield due to lo\\ temperature during the winter season (December to February} decreased in the range of about 8% to 40% depending on the clones Low temperatureinduced yield depression was lowest in clone RRIM 600 which indicated its relatively better acclimatisation to the cold climate Latex thiol content increased about five-fold in the winter season in comparison to the peak yielding pre-winter season This remarkable increase in thiol content in the latex in the wmtei season confirmed a positive relation between thiol and cold stress in Hevea for the first time Sugai and thiol were found negatively correlated with yield Positive correlations were obtained between yield and maximum temperature (TmaJ, minimum temperature (Tmll), the total solid content of latex (TSC) and soil moisture (SM) A multiple regression analysis considering the yield as dependent and sugat thiol inorganic phosphate (Pi), TSC, T^, TmiK and SM as independent variables revealed that about 41% variability of yield can be explained through these independent variables Path coefficient analysis proved that thiol, Pi, TSC and SM have major direct effects on yield while Pi, TSC, Tmn and SMweie noted to have direct effects on thiol Strong relations of thiol with yield and minimum temperature showed that the ratio of yield to thiol would be one of the determinants for rubber producing potential of Hevea clones during winter in the non-optimal environment
Inheritance Study of Aphid ( Aphis craccivora KOCH) and Rosette Resistance in Groundnut ( Arachis hypogaea L .)

This study was conducted to investigate the gene effects, heritability, genetic advance and number of effective factors controlling the inheritance of aphid and rosette resistance and other quantitative characters. Two aphid resistance, one rosette resistance, one aphid susceptible and one rosette susceptible lines were used as parents to develop F1s, F2s, BC1P1 and BC1P2. The seventeen generations obtained were evaluated along with three checks in three replications using randomized complete block design. The three parameter model was adequate to explain variations observed in the inheritance of days to fifty percent flowering, plant height, number of seeds per plant and shelling percentage. Non allelic interaction was significant with high narrow-sense heritability as obtained for rosette disease incidence, rosette severity index, number of matured pods per plant and net pod yield. It is possible to expect advance for these characters in further segregating generations. Wide ranges of narrow and broad sense heritability accompanied with moderate to high genetic advance except for aphid infestation index were obtained for the characters studied. The number of effective factors revealed that the understudied characters were governed by mono, oligo, and polygenes.
Gene expression changes during female reproductive development in a colour polymorphic insect

Pleiotropy (multiple phenotypic effects of single genes) and epistasis (gene interaction) play key roles in the development of complex phenotypes and might be especially important in polymorphic taxa. The development of discrete and heritable sympatric phenotypic polymorphisms often emerges from major-effect genes that interact with other loci and have pleiotropic effects on multiple traits and physiological functions. We quantified gene expression changes during ontogenetic colour development in an insect (damselfly: Ischnura elegans) with three heritable female colour morphs, one which is a male mimic. Using transcriptome sequencing and de novo assembly, we demonstrate that all morphs show extensive downregulation of gene expression during early colour development. Morphs then become increasingly differentiated during sexual maturation and when developing adult colouration. These different ontogenetic trajectories arise because of the heterochronic development of the male-mimicking females, compared to other two female morphs. Many loci with regulatory functions in reproductive development are uniquely regulated in male-mimicking females, including upstream and downstream regulators of ecdysone signalling and transcription factors that influence insect sexual differentiation. Our study reveals extensive epistasis in the genomic architecture of I. elegans and suggest a central role for pleiotropy in shaping the developmental trajectories of the different morphs.
Clonación, expresión y caracterización de la toxina de tres dedos Mipartoxin-I, Mayor componente toxico del veneno de Micrurus mipartitus (serpiente coral rabo de ají).

Cinco secuencias precursoras para la familia de las alfa-neurotoxinas de cadena corta fueron identificadas a partir del ADNc de la glandula venenosa de la Micrurus mipartitus (serpiente coral rabo de aji). Entre ellas la secuencia precursora para la Mipartoxin-I, la Mipartoxin-Ia, isoforma de la anterior, y 3 proteinas mas las cuales fuero denominadas Mipartoxin-II, Mipartoxin-III y Mipartoxin-IV. Estas secuencias codificaron para un propeptido de 79-82 aminoacidos, el cual contiene un peptido senal de 21 aminoacidos y un peptido maduro entre 58-61 aminoacidos. A partir de la secuencia codificante para la Mipartoxin-I, se clonaron tres constructos en el plasmido pPICzαC en Pichia pastoris cepa X33: Mipartoxin-IA (secuencia propeptido Mipartoxin-I), Mipartoxin-IB (secuencia Mipartoxin-I), y Mipartoxin-IC (secuencia Mipartoxin-I mas epitopo c-myc y marcador de 6 histidinas). Sin embargo solamente la Mipartoxin-IC fue la que evidencio una produccion aceptable con una concentracion de 2-5 mg/L de proteina recombinante con una pureza de 95%. No obstante no mostro efecto letal en el modelo de raton, pero indujo una leve toxicidad a 100ug/raton. Por analisis de digestion con tripsina en gel por MALDI-TOF-TOF se confirmaron peptidos de la Mipartoxin-IC, igualmente por anticuerpos anti-His se confirmo la expresion de la proteina. Finalmente por migracion en SDS-PAGE y LS/MSD se determino que su masa molecular fue de 11.715 Da.
Insights into actin polymerization and nucleation using a coarse grained model

We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the Cα atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, X-ray diffraction and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at tilted conformations and the barbed end tilt range was dependent on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to the antiparallel (lower) dimer. Individual monomers bound each other in a short-pitch helix complex in addition to other configurations, with several of them apparently non-productive for polymerization. Simulations with multiple monomers in the F-actin form reproduce filamentation as well as transient aggregates at the barbed end. We discuss the implications on the kinetic pathway of actin filament nucleation and polymerization and possibilities for future improvements of the coarse-grained model. SIGNIFICANCE Control of actin filament polymerization and nucleation has crucial importance to cellular life. We show that coarse-grained molecular dynamics simulations are a powerful tool which can gauge involved mechanisms at reasonable computational cost, while retaining essential features of the fully atomic, yet less computationally tractable, system. Using a knowledge-based potential demonstrates the power of these methods at explaining and reproducing polymerization. Intermediate actin complexes identified in the simulations may play critical roles in the kinetic pathways of actin polymerization which may have been difficult to observe in prior experiments. These methods have been sparsely applied to the actin system, yet have potential to answer many important questions in the field.