Miracle-dz/UniFAR-FTUs huggingface dataset:
Covalent perturbation as a tool for validation of identifications and PTM mapping applied to bovine alpha‐crystallin

Proteomic identifications hinge on the measurement of both parent and fragment masses and matching these to amino acid sequences via database search engines. The correctness of the identifications is assessed by statistical means. Here we present an experimental approach to test identifications. Chemical modification of all peptides in a sample leads to shifts in masses depending on the chemical properties of each peptide. The identification of a native peptide sequence and its perturbed version with a different parent mass and fragment ion masses provides valuable information. Labeling all peptides using reductive alkylation with formaldehyde is one such perturbation where the ensemble of peptides shifts mass depending on the number of reactive amine groups. Matching covalently perturbed fragmentation patterns from the same underlying peptide sequence increases confidence in the assignments and can salvage low scoring post‐translationally modified peptides. Applying this strategy to bovine alpha‐crystallin, we identify 9 lysine acetylation sites, 4 O‐GlcNAc sites and 13 phosphorylation sites.
Altered parietal brain oxygenation in Alzheimer's disease as assessed with near-infrared spectroscopy.

OBJECTIVE Visuospatial deficits are among the first symptoms of Alzheimer disease (AD) and linked to lower activation in the superior parietal cortex as assessed with functional imaging. Near-infrared spectroscopy (NIRS) is an optical method to measure changes in the concentration of oxygenated hemoglobin and deoxygenated hemoglobin in the microvascular system of the cortex. Because of its advantages in measurement situation, NIRS has proven to be especially suited for investigating psychiatric patients. The aim of this study was to probe the activation of parietal regions in patients with AD, performing a visuospatial task by means of functional NIRS (fNIRS). METHODS Thirteen patients with suspected mild AD and 13 healthy subjects comparable in age and gender were investigated while working on a modified version of the Benton Line Orientation Task. RESULTS During the spatial task, healthy subjects showed explicit parietal activation, whereas patients displayed only activation during the control task. Interestingly, there was no difference in visuospatial performance between the two groups. CONCLUSION The results indicate that fNIRS is able to measure parietal activation deficits in patients with AD, which could be developed into an early detection method in the future.
Amplification of long targets of approximately 50 kb from cloned cosmid inserts of Arabidopsis thaliana.

Since the robust amplification of targets greater than approximately 5 kb has been reported, the long polymerase chain reaction (PCR) method has become a labor-saving alternative cloning method in the analysis of larger genomic segments. ~ This method has been used to amplify up to 22 kb of human genomic DNA, 42 kb from the genome of A bacteriophage, and 16.3 kb of the 16.6-kb human mitochondrial genome. No reports on the amplification of long targets from cloned cosmid inserts as templates have been published, however. In the present study, we report the amplification of long targets up to approximately 50 kb from cloned cosmid inserts of Arabidopsis thaliana. Five cosmid clones that constitute a contig near the abil locus on chromosome 4 of A. thaliana,' were used as templates for the amplification of inserted DNA fragments. Escherichia coli cells containing cosmid clones were grown for 16 h at 37°C while being shaken at 200 rpm in super broth (SB) medium supplemented with 50 (Ug/ml ampicillin. Cosmid DNA templates were then prepared using the Automatic Plasmid Isolation System (Model PI-100, KURABO, Osaka, Japan) and purified using the Qiagen Plasmid Mini Kit (Qiagen Inc., CA, USA) according to the manufacturer's instructions. The amplification of inserts was performed using the Takara LA PCR Kit Ver. 2 (Takara Shuzo Co., Kyoto, Japan) in a THERMAL SEQUENCER TSR-300 (IWAKI GLASS Co., Ltd., Chiba, Japan). The reaction mixture (50 iA) consisted of 20 ng of cosmid DNA, 1 x LA PCR buffer II (Mg plus), 400 mM dNTP, 0.2 fiM of each primer, and 1.5 units of Takara LA Taq. Primers were chosen from the /3-lactamase gene and the 5' flanking region of the 70 K heat-shock gene; regions flanking the cloning sites of the cosPneo cosmid vector. Primer sequences were 5'-CGGGGCGAAAACTCTCAAGGATCTTACCGC-3' (cosPneoF4) and 5'-CAGAGTGAGAGAGCATTAGTGCAGAGAGGG-3' (cosPneoRl). Thermal cycling profiles consisted of 30 cycles of denaturation at 99° C for 45 s and annealing and extension at 68°C for 30 min. All the
Properties of K+ and Cl- channels and their involvement in proliferation of rat microglial cells.

Essentially pure (>95%) cultures of microglia were established from neopallia of newborn rats and used for whole-cell patch-clamp recording of electrophysiological properties and for proliferation studies. Two types of cultures were examined: 1) "Primary" cultures were grown in culture medium with serum and used within 3 weeks of isolation; 2) and "Colony-stimulating factor (CSF)-1-stimulated" cultures were derived from 3-week-old "primary" cultures by passaging and culturing them for several weeks longer in the presence of conditioned medium enriched in CSF-1. Microglia in the "primary" cultures expressed: 1) an inwardly rectifying K+ current (Kir) that was inhibited by Ba2+; 2) an outwardly rectifying K+ current (Kv) with many similarities to the cloned Kv1.3 channel of lymphocytes, including block by nanomolar concentrations of charybdotoxin (ChTX) and margatoxin (MgTX); and 3) an outwardly rectifying anion current with time- and voltage-independent gating. The anion current is activated reversibly under cell swelling conditions, i.e., after exposure to a hypo-osmotic bathing medium. The anion channels are highly permeable to Cl-, measurably permeable to gluconate (P(gluconate)/ PCl = 0.34), and blocked by flufenamic acid, 4-nitro-2-(3-phenylpropylamino)- benzoic acid (NPPB), and 6, 7-dichloro-2-cyclopentyl-2, 3-dihydro-2-methyl-1-oxo-1H-inden-5-yl (oxy) acetic acid (IAA-94). Microglia in the "CSF-1-stimulated" cultures expressed Kir and Cl- current, but not Kv current. Proliferation in the latter type of cultures could be slowed by omission of the CSF-1 enriched supernatant for 2 days and stimulated by adding back the conditioned medium. This "CSF-1-stimulated" proliferation was inhibited by Ba2+ (Kir blocker), and the Cl(-)-channel blockers flufenamic acid, NPPB, and IAA-94, whereas the Kv blockers ChTX and MgTX had no effect. Thus, Kir and Cl- channels appear to be necessary for "CSF-1-stimulated" proliferation of rat microglia, and there is no evidence that even a transient activation of Kv is necessary.
Effects of 10 days of separate heat and hypoxic exposure on heat acclimation and temperate exercise performance.

Adaptations to heat and hypoxia are typically studied in isolation but are often encountered in combination. Whether the adaptive response to multiple stressors affords the same response as when examined in isolation is unclear. We examined 1) the influence of overnight moderate normobaric hypoxia on the time course and magnitude of adaptation to daily heat exposure and 2) whether heat acclimation (HA) was ergogenic and whether this was influenced by an additional hypoxic stimulus. Eight males [V̇o2max = 58.5 (8.3) ml·kg-1·min-1] undertook two 11-day HA programs (balanced-crossover design), once with overnight normobaric hypoxia (HAHyp): 8 (1) h per night for 10 nights [[Formula: see text] = 0.156; SpO2 = 91 (2)%] and once without (HACon). Days 1, 6, and 11 were exercise-heat stress tests [HST (40°C, 50% relative humidity, RH)]; days 2-5 and 7-10 were isothermal strain [target rectal temperature (Tre) ~38.5°C], exercise-heat sessions. A graded exercise test and 30-min cycle trial were undertaken pre-, post-, and 14 days after HA in temperate normoxia (22°C, 55% RH; FIO2 = 0.209). HA was evident on day 6 (e.g., reduced Tre, mean skin temperature (T̄sk), heart rate, and sweat [Na+], P < 0.05) with additional adaptations on day 11 (further reduced T̄sk and heart rate). HA increased plasma volume [+5.9 (7.3)%] and erythropoietin concentration [+1.8 (2.4) mIU/ml]; total hemoglobin mass was unchanged. Peak power output [+12 (20) W], lactate threshold [+15 (18) W] and work done [+12 (20) kJ] increased following HA. The additional hypoxic stressor did not affect these adaptations. In conclusion, a separate moderate overnight normobaric hypoxic stimulus does not affect the time course or magnitude of HA. Performance may be improved in temperate normoxia following HA, but this is unaffected by an additional hypoxic stressor.
Membrane regulation of the chromosomal replication activity of E.coli DnaA requires a discrete site on the protein.

The capacity of DnaA protein to initiate DNA synthesis at the chromosomal origin is influenced profoundly by the tightly bound nucleotides ATP and ADP. Acidic phospholipids can catalyze the conversion of inactive ADP‐DnaK protein into the active ATP form. Proteolytic fragments of the nucleotide form of DnaA protein were examined to determine regions of the protein critical for functional interaction with membranes. A 35 kDa chymotryptic and 29 kDa tryptic fragment retained the tightly bound nucleotide. The fragments, whose amino‐termini are within three residues of each other, but differ at their carboxyl ends, showed strikingly different behavior when treated with acidic phospholipids. The larger chymotryptic fragment released the bound nucleotide in the presence of acidic, but not neutral phospholipids. In contrast, the smaller tryptic fragment was inert to both forms of phospholipids. Acidic membranes, but not those composed of neutral phospholipids, protect from tryptic digestion a small portion of the segment that constitutes the difference between the 29 and 35 kDa fragments. The resulting 30 kDa tryptic fragment, which possesses this protected region, interacts functionally with acidic membranes to release the bound effector nucleotide. Inasmuch as the anionic ganglioside GM1, a compound structurally dissimilar to acidic glycerophospholipids, efficiently releases the nucleotide from DnaA protein, an acidic surface associated with a hydrophobic environment is the characteristic of the membrane that appears crucial for regulatory interaction with DnaA protein.
Placental Abruption Following Placement of Disposable Intrauterine Pressure Transducer System

There have been few reported complications of intrauterine pressure monitoring. We present four cases of placental abruption following insertion of a disposable intrauterine pressure transducer system (INTRAN). All four patients had placental abruptions, which were evident soon after insertion of the disposable intrauterine pressure transducer system (all of our cases had predisposing factors or signs of placental abruption at presentation). Whether there was a preexisting placental abruption, which was caused, revealed, or worsened by insertion of the disposable intrauterine pressure transducer system is unclear. We encourage careful patient selection with gentle insertion of the system opposite the placental site.
Effects of a Pulmonary Rehabilitation Program With Balance Training on Patients With COPD

PURPOSE: Patients with chronic obstructive pulmonary disease (COPD) have balance impairments. However, pulmonary rehabilitation (PR) is associated with only minor improvements in functional balance. Therefore, there is a need to explore the role of balance training within PR. This study aimed at assessing the effects of a PR program, with a specific component of balance training, on functional balance of patients with COPD. METHODS: Outpatients with COPD (N = 22, age = 68.0 ± 11.8 years; forced expiratory volume in 1 second = 72.2 ± 22.3% predicted) participated in a 12-week PR program including exercise training and psychosocial support and education. Exercise training sessions comprised endurance, strength, and a specific component of balance training. The Timed Up and Go (TUG) test was used to assess functional balance before and after the PR. Health-related quality of life (St George's Respiratory Questionnaire), quadriceps muscle strength (10 repetition maximum), and exercise tolerance (6-minute walk test) were also assessed. RESULTS: Patients demonstrated significant improvements in TUG scores after PR (mean change −1.7 ± 1.4 seconds; P = .001; effect size = 1.249). Before PR, 9 (41%) participants and after PR only 1 (4.5%) participant had a TUG performance worse than the average performance of age-matched healthy peers (P = .008). The St George's Respiratory Questionnaire symptoms score (P = .012), quadriceps muscle strength (P = .001), and exercise tolerance (P = .001) were also improved. CONCLUSIONS: Pulmonary rehabilitation with a specific component of balance training had a large effect on functional balance in patients with COPD. Findings highlight the value of including balance training in PR programs. Further research is needed to determine the optimal intervention to improve balance and its specific components among patients with COPD.
Hybrid intravascular imaging: recent advances, technical considerations, and current applications in the study of plaque pathophysiology

Cumulative evidence from histology-based studies demonstrate that the currently available intravascular imaging techniques have fundamental limitations that do not allow complete and detailed evaluation of plaque morphology and pathobiology, limiting the ability to accurately identify high-risk plaques. To overcome these drawbacks, new efforts are developing for data fusion methodologies and the design of hybrid, dual-probe catheters to enable accurate assessment of plaque characteristics, and reliable identification of high-risk lesions. Today several dual-probe catheters have been introduced including combined near infrared spectroscopy-intravascular ultrasound (NIRS-IVUS), that is already commercially available, IVUS-optical coherence tomography (OCT), the OCT-NIRS, the OCT-near infrared fluorescence (NIRF) molecular imaging, IVUS-NIRF, IVUS intravascular photoacoustic imaging and combined fluorescence lifetime-IVUS imaging. These multimodal approaches appear able to overcome limitations of standalone imaging and provide comprehensive visualization of plaque composition and plaque biology. The aim of this review article is to summarize the advances in hybrid intravascular imaging, discuss the technical challenges that should be addressed in order to have a use in the clinical arena, and present the evidence from their first applications aiming to highlight their potential value in the study of atherosclerosis.
Enterococcus cecorum osteomyelitis and arthritis in broiler chickens

Starting from December 2006, Enterococcus cecorum infections with a clinical course have increasingly been observed in Belgian broilers. The present paper describes the characteristics of the disease on the basis of observations in 10 different farms. The affected chicks always suffered from paresis and lameness. Onset of the signs was usually within the first 2 weeks of life, and it resulted in up to 7% increased mortality starting from day 21-32. The cocks were affected significantly more often than the hens. Lesions of osteomyelitis of the caudal thoracic vertebrae compressing the spinal cord and/or arthritis of the hock joints were consistently found. E. cecorum was always isolated from these lesions. The disease was recurrent in successive rounds in 9 out of the 10 farms. Antibiotic treatment was only successful when initiated preventively from the first week of life onwards. Other infections often associated with similar signs were not detected. It can be concluded that E. cecorum infections form an important emerging disease in broilers, leading to high mortality rates.
A Machine Learning Approach to Non-uniform Spatial Downscaling of Climate Variables

This study presents a scalable and robust approach to spatial downscaling in the context of climate downscaling. We explore the ability of four techniques to downscale a climate variable to a given location of interest. As an example, we focus on downscaling daily mean air temperature at twelve stations located across the topographically complex province of British Columbia, Canada. The techniques include multi-linear regression (MLR), artificial neural networks (ANN), extreme learning machines (ELM) and long-short term memory networks (LSTM). Our method based on LSTM generalizes well to different locations and leads to higher downscaling accuracy compared to MLR and ELM. The performance of the models is measured based on statistical metrics, including the coefficient of determination, and the root mean square error.
Protein complex identification by graph local clustering and use of Chou's amphiphilic Pseudo amino-acid features

The intend of this paper is to introduce a new method for protein complex identification. Proteins share an important role by signaling cells. Proteins are three dimensional objects and any types of deformed proteins can cause severe disease, because their function is related to their shape and also the amino-acid sequence they have coded with. Technically speaking similar types of proteins tend to act by forming a group or a complex and if we can find a highly accurate way to identify the complexes we can find a group of proteins that are responsible for something. For this purpose different types of algorithms have proposed but most of them failed to achieve enough precision. Here we will use a new method which uses Chou Pseudo amino-acid as a set of features and we will get a good result even by using machine learning techniques that were supposed as not an effective tool in this field before.
Evolutionary Grid Scheduling Algorithm with Predictive Resource Optimization

Optimal assigning jobs to resources is an important problem in grid computing. Now grid scheduling policies are mostly traditional heuristic algorithms for scheduling n independent tasks on m processors in early finishing time. However grids have developed to wide area, heterogeneous and non autonomous environments, business objective also became crucial for the success of the scheduling. Therefore base on a grid scheduling model with business parameters, we designed an evolutionary scheduling algorithm. The algorithm capability and performance were demonstrated by simulations. Furthermore a predictive resource mechanism was brought out to improve scheduling efficiency. At last we presented implementation scenario of our algorithm with predictive resource optimization in wide area open grid.
BACKPROPOGATION NEURAL NETWORK FOR PREDICTION OF HEART DISEASE

Recently, several software’s, tools and various algorithms have been proposed by the researchers for developing effective medical decision support systems. Moreover, new algorithms and new tools are continued to develop and represent day by day. Diagnosing of heart disease is one of the important issue and many researchers investigated to develop intelligent medical decision support systems to improve the ability of the physicians. Neural network is widely used tool for predicting heart disease diagnosis. In this research paper, a heart disease prediction system is developed using neural network. The proposed system used 13 medical attributes for heart disease predictions. The experiments conducted in this work have shown the good performance of the proposed algorithm compared to similar approaches of the state of the art.
Stochastic Recursive Gradient Algorithm for Nonconvex Optimization

In this paper, we study and analyze the mini-batch version of StochAstic Recursive grAdient algoritHm (SARAH), a method employing the stochastic recursive gradient, for solving empirical loss minimization for the case of nonconvex losses. We provide a sublinear convergence rate (to stationary points) for general nonconvex functions and a linear convergence rate for gradient dominated functions, both of which have some advantages compared to other modern stochastic gradient algorithms for nonconvex losses.
Process simulation of Junctionless transistor for low power applications

This proposed Technique deals with the process simulation of a Junctionless transistor which will overcome the drawbacks faced by Fabrication engineers. It also compares the performance of both single gate and multigate Junctionless transistors. All existing transistors are based on the use of semiconductor junctions formed by introducing dopant atoms into the semiconductor material. As the distance between junctions in modern devices drops below 10 nm, extraordinarily high doping concentration gradients become necessary. Because of the laws of diffusion and the statistical nature of the distribution of the doping atoms, such junctions represent an increasingly difficult fabrication challenge for the semiconductor industry. Here, we propose and demonstrate a new type of transistor in which there are no junctions and no doping concentration gradients. These devices have full CMOS functionality and are made using silicon nanowires. They have near-ideal subthreshold slope, extremely low leakage currents, and less degradation of mobility with gate voltage and temperature than classical transistors. The main focus of this project work is to analyze the transistor parameters without going for real time fabrication. The parameters ideal for a good device is obtained by changing them with certain values. Using this process simulation, the errors in the device fabrication can be reduced.
Multiple Genetically Distinct Groups Revealed among Clinical Isolates Identified as Atypical Aspergillus fumigatus

ABSTRACT To investigate whether genetic variants of A. fumigatus are found among clinical isolates, four isolates that were originally identified as poorly sporulating strains of Aspergillus fumigatus were subjected to molecular analysis. DNA sequence analysis of the alkaline protease genes of these isolates showed that each is genetically distinct and each shows substantial variation (7 to 11%) from the A. fumigatus nucleotide sequence. Subsequent morphological examination suggested that all of the isolates could be classified as Aspergillus viridinutans. To clarify the taxonomic status of these four clinical isolates and of two previously identified as atypical A. fumigatus isolates, partial β-tubulin and 18S rRNA gene sequences were determined. Each of the six atypical strains had a unique β-tubulin sequence, whereas the sequences of three standard isolates of A. fumigatus, which were included as controls, were identical to the published A. fumigatus β-tubulin sequence. The very low level of DNA sequence variation detected in standard isolates of A. fumigatus compared with other isolates from members of Aspergillus section Fumigati suggests that it may be a relatively recently evolved species. The 18S rRNA gene of two of the atypical isolates differed from that of A. fumigatus at a single nucleotide position. Phylogenetic analyses do not support the classification of all of these isolates as A. viridinutans. Thus, some of these isolates represent new species which are potential opportunistic pathogens.
Extremely Low-Frequency Magnetic Field Exposure and Protection Against UV-Induced Death in Chicken Embryos

We report on a study where 4-day old chicken embryos from different flocks were pre-treated with 50 Hz magnetic fields (MF) prior to a 60-min UV-C exposure (1.7 mW/cm2) to investigate the possible protective effect of MF exposure on UV-induced embryo death. Different flux densities (0.010, 0.025, 0.050, 0.10, and 0.20 mT), field directions (vertical and horizontal), as well as MF exposure times (10, 20, and 60 min) were employed. We did not find any significant effects by MF exposure, irrespective of exposure time, flux density, or field direction on the survival of embryos. Neither could we find any flock dependency on sensitivity to MF exposure.