Miracle-dz/UniFAR-FTUs huggingface dataset:
2-Hydroxyisobutyrylation on histone H4K8 is regulated by glucose homeostasis in Saccharomyces cerevisiae

Significance DNA–histone complexes are packed into the eukaryotic genome and fit into the nucleus of the cell. One mechanism to access the genetic information is to disrupt the complexes through posttranslational modification of histones. Recently, histone H4K8 2-hydroxyisobutyrylation (H4K8hib) was identified as an evolutionarily conserved active mark. However, how this modification is regulated and what are the enzymes to modulate this modification within a cell remain a mystery. In this study, we discover that this modification is regulated by the availability of a carbon source in Saccharomyces cerevisiae and identify the enzymes catalyzing the removal of this active mark in vivo. This discovery provides insight into the function and regulation of the histone mark H4K8hib. New types of modifications of histones keep emerging. Recently, histone H4K8 2-hydroxyisobutyrylation (H4K8hib) was identified as an evolutionarily conserved modification. However, how this modification is regulated within a cell is still elusive, and the enzymes adding and removing 2-hydroxyisobutyrylation have not been found. Here, we report that the amount of H4K8hib fluctuates in response to the availability of carbon source in Saccharomyces cerevisiae and that low-glucose conditions lead to diminished modification. The removal of the 2-hydroxyisobutyryl group from H4K8 is mediated by the histone lysine deacetylase Rpd3p and Hos3p in vivo. In addition, eliminating modifications at this site by alanine substitution alters transcription in carbon transport/metabolism genes and results in a reduced chronological life span (CLS). Furthermore, consistent with the glucose-responsive H4K8hib regulation, proteomic analysis revealed that a large set of proteins involved in glycolysis/gluconeogenesis are modified by lysine 2-hydroxyisobutyrylation. Cumulatively, these results established a functional and regulatory network among Khib, glucose metabolism, and CLS.
The validity of anesthetic protocols for the surgical procedure of castration in rats

To achieve surgical anesthesia in animal experimentation, it is necessary to select the appropriate anesthetic protocol by considering its pharmacological properties and the surgical procedure to be performed. However, few studies have investigated the validity of anesthetic protocols under surgical conditions in small rodents. The present study aimed to clarify the pharmacological properties of 4 anesthetic protocols during the surgical procedure of castration in rats. Eight-week-old male Wistar rats were anesthetized with anesthetics, including the combination of ketamine and xylazine (K/X), the combination of medetomidine, midazolam, and butorphanol (M/M/B), isoflurane, and sevoflurane. Castration was performed under each anesthesia, and anesthetic depth and times were assessed, as were vital signs. The injectable anesthetics were investigated at standard and high doses. The concentration of inhalant anesthetics was adjusted to 1.5 minimum alveolar concentration (MAC). K/X at both doses demonstrated sufficient anesthetic depth with rapid induction and recovery. However, bradycardia and hypothermia were prominent in high-dose K/X, indicating that the standard-dose is more appropriate for surgical anesthesia in castration procedures. M/M/B demonstrated high anesthetic sensitivity variation in individual animals. In contrast to injectable anesthetics, inhalant anesthetics provided stable anesthetic depth with less cardiorespiratory influence. Sevoflurane did not lead to a significant decrease in rectal temperature during the anesthetic period. Results of the present study revealed the optimal dose and pharmacological features of several anesthetic protocols for castration, and may contribute to the standardization of surgical anesthesia in rats.
The Deubiquitinating Enzyme Ataxin-3, a Polyglutamine Disease Protein, Edits Lys63 Linkages in Mixed Linkage Ubiquitin Chains*

Ubiquitin chain complexity in cells is likely regulated by a diverse set of deubiquitinating enzymes (DUBs) with distinct ubiquitin chain preferences. Here we show that the polyglutamine disease protein, ataxin-3, binds and cleaves ubiquitin chains in a manner suggesting that it functions as a mixed linkage, chain-editing enzyme. Ataxin-3 cleaves ubiquitin chains through its amino-terminal Josephin domain and binds ubiquitin chains through a carboxyl-terminal cluster of ubiquitin interaction motifs neighboring the pathogenic polyglutamine tract. Ataxin-3 binds both Lys48- or Lys63-linked chains yet preferentially cleaves Lys63 linkages. Ataxin-3 shows even greater activity toward mixed linkage polyubiquitin, cleaving Lys63 linkages in chains that contain both Lys48 and Lys63 linkages. The ubiquitin interaction motifs regulate the specificity of this activity by restricting what can be cleaved by the protease domain, demonstrating that linkage specificity can be determined by elements outside the catalytic domain of a DUB. These findings establish ataxin-3 as a novel DUB that edits topologically complex chains.
Evidence for Long-Timescale Patterns of Synaptic Inputs in CA1 of Awake Behaving Mice

Repeated sequences of neural activity are a pervasive feature of neural networks in vivo and in vitro. In the hippocampus, sequential firing of many neurons over periods of 100–300 ms reoccurs during behavior and during periods of quiescence. However, it is not known whether the hippocampus produces longer sequences of activity or whether such sequences are restricted to specific network states. Furthermore, whether long repeated patterns of activity are transmitted to single cells downstream is unclear. To answer these questions, we recorded intracellularly from hippocampal CA1 of awake, behaving male mice to examine both subthreshold activity and spiking output in single neurons. In eight of nine recordings, we discovered long (900 ms) reoccurring subthreshold fluctuations or “repeats. ” Repeats generally were high-amplitude, nonoscillatory events reoccurring with 10 ms precision. Using statistical controls, we determined that repeats occurred more often than would be expected from unstructured network activity (e.g., by chance). Most spikes occurred during a repeat, and when a repeat contained a spike, the spike reoccurred with precision on the order of ≤20 ms, showing that long repeated patterns of subthreshold activity are strongly connected to spike output. Unexpectedly, we found that repeats occurred independently of classic hippocampal network states like theta oscillations or sharp-wave ripples. Together, these results reveal surprisingly long patterns of repeated activity in the hippocampal network that occur nonstochastically, are transmitted to single downstream neurons, and strongly shape their output. This suggests that the timescale of information transmission in the hippocampal network is much longer than previously thought. SIGNIFICANCE STATEMENT We found long (≥900 ms), repeated, subthreshold patterns of activity in CA1 of awake, behaving mice. These repeated patterns (“repeats”) occurred more often than expected by chance and with 10 ms precision. Most spikes occurred within repeats and reoccurred with a precision on the order of 20 ms. Surprisingly, there was no correlation between repeat occurrence and classical network states such as theta oscillations and sharp-wave ripples. These results provide strong evidence that long patterns of activity are repeated and transmitted to downstream neurons, suggesting that the hippocampus can generate longer sequences of repeated activity than previously thought.
Galanin-like immunoreactivity is influenced by estrogen in peripubertal and adult rats.

Galanin gene expression in the anterior pituitary is potently stimulated by estrogen in adult rats. To evaluate the influence of estrogen on galanin during the peripubertal period 30- to 32-day-old female rats were treated with pregnant mare serum gonadotropin (PMSG, 10 IU s.c., 10.00 h). Galanin-like immunoreactivity (galanin-LI) in hypothalamic and pituitary tissues was evaluated 1, 2 or 3 days after PMSG treatment between 17.00 and 19.00 h. The PMSG treatment stimulated 17 beta-estradiol secretion, which induced a midafternoon LH surge 2 days after the PMSG treatment. Concentrations of galanin-LI at the time of this LH surge were elevated 82% in the anterior pituitary and 58% in the hypothalamus (without the median eminence) when compared to saline-treated female rats. On the 3rd day after the PMSG injection, galanin-LI was increased 236% in the anterior pituitary, 88% in the neurointermediate lobe and 39% in the median eminence compared to saline-treated female rats. These changes in galanin-LI were not observed in similarly aged male rats or ovariectomized rats treated with PMSG. In adult male rats, daily injections with 17 beta-estradiol valerate (10 micrograms/daily s.c.) for 1 week increased galanin-LI in the median eminence and neurointermediate lobe to an extent similar to that seen in juvenile female rats following PMSG treatment. In contrast, the high serum levels of 17 beta-estradiol achieved after 17 beta-estradiol valerate treatment increased galanin-LI in the anterior pituitary 65-fold. These studies indicate that galanin-LI is influenced by estrogen in peripubertal and adult rats. (ABSTRACT TRUNCATED AT 250 WORDS)
Corrosion–Fatigue Life Prediction for 2024-T62 Aluminum Alloy Using Damage Mechanics-Based Approach

An approach based on the continuum damage mechanics was applied to predict corrosion–fatigue crack initiation life of 2024-T62 aluminum alloy. A fatigue test in air, a pre-corrosion–fatigue test, and a corrosion–fatigue test on smooth standard specimens were performed. The fatigue lives are strongly reduced by the corrosive environment of 5 wt. % NaCl continuous salt spray compared with non-corroded specimens. Damage evolution models for fatigue in air and pre-corrosion–fatigue of smooth specimens were established, which forms the basis for solving the corrosion–fatigue problem. Finally, the method of corrosion–fatigue life prediction was presented. The predictions comply with the experimental data.
Protein analysis in cerebrospinal fluid. III. Relation to blood-cerebrospinal fluid barrier function for formulas for quantitative determination of intrathecal IgG production.

To examine the possible influence of the blood-CSF barrier function on mathematical formulas for estimating intrathecal IgG production (IgG index, Tourtellotte's formula [TOURT], Schuller and Sagar's formula [Schull], and Reiber and Felgenhauer's formula [IgG(loc)]), we analysed serum and CSF samples from 105 healthy individuals, aged 18-88 years, and 816 consecutive patients without oligoclonal IgG bands (OCBs) in the CSF, aged 18-91 years. In healthy individuals there was no significant correlation between the CSF/serum (S) albumin ratio (i.e. blood-CSF barrier function) and the IgG index, a dimensionless quotient for determining intrathecal IgG production, and only a small correlation (r = -0.08, p < 0.05) in patients without OCBs. However, significant dependence on the blood-CSF barrier function was found, in both healthy individuals and patients without OCBs, for the formulas determining intrathecal IgG production in milligrams (per litre CSF or per day), i.e. for TOURT, SCHULL and IgG(loc). Therefore, we propose a new formula for the quantitative determination of intrathecal IgG production in mg/l, the IGGPROD, which is calculated as: CSF-IgG -[(0.51 x CSF-Alb x S-IgG)/S-Alb]. IGGPROD is an empirical formula, based on findings in 105 healthy individuals 18-88 years of age, and does not depend on the blood CSF barrier function.
Attitudes and Perceptions Related to Smoking among Pregnant and Postpartum Women in a Low-Income, Multiethnic Setting

Purpose. The purpose of this study was to gain insight into attitudes and perceptions about smoking during pregnancy, passive smoke exposure, barriers to quitting, and program preferences among women in a low-income, ethnically diverse setting. Design. Nine focus group discussions were conducted with African-American, Native American, and white women. Discussions were moderated by local residents who shared the same ethnic background as group participants. Setting. Discussions were held in neighborhood centers and clinics in an urban area. Subjects. A total of 57 women participated. Moderators recruited participants from within their social networks and from neighborhood programs. The informal process of recruitment did not allow calculation of response rates. Measures. A series of open-ended questions with selected probes was used to guide the conversation. Results. Participants were aware that smoking during pregnancy is harmful and were concerned to varying degrees about their smoking behavior. Most women who smoked took active steps to reduce the risks. Actions were frequently accompanied by beliefs that rationalized moderate levels of smoking. While concerned, women were uncertain about what constituted harmful, passive smoke exposure. Personal barriers to quitting included being around others who smoked, feelings of stress and boredom, addiction, and not believing smoking is dangerous enough. Participants tended to value pregnancy-related advice from female friends and relatives over advice from professionals. Conclusions. Results suggest that many women respond to warnings about smoking during pregnancy, but actions are not necessarily measured, in quit rates. Misconceptions about the risks may help to rationalize continued smoking. Subjects lacked knowledge about how best to reduce the risks of passive smoke. Educational efforts may be effective when directed at networks of women who share information. The nature of qualitative data collection prevents extrapolation of these results to a larger population.
A Pilot Study of Immune Activation and Rifampin Absorption in HIV-Infected Patients without Tuberculosis Infection: A Short Report

Background Rifampin malabsorption is frequently observed in tuberculosis patients coinfected with human immunodeficiency virus (HIV) but cannot be predicted by patient factors such as CD4+ T cell count or HIV viral load. Methods We sought to describe the relationship between HIV-associated immune activation, measures of gut absorptive capacity and permeability, and rifampin pharmacokinetic parameters in a pilot study of 6 HIV-infected, tuberculosis-uninfected patients who were naïve to antiretroviral therapy. Results The median rifampin area under the concentration-versus-time curve during the 8-hour observation period was 42.8 mg·hr/L (range: 21.2 to 57.6), with a median peak concentration of 10.1 mg/L (range: 5.3 to 12.5). We observed delayed rifampin absorption, with a time to maximum concentration greater than 2 hours, in 2 of 6 participants. There was a trend towards increased plasma concentrations of sCD14, a marker of monocyte activation in response to bacterial translocation, among participants with delayed rifampin absorption compared to participants with rapid absorption (p = 0.06). Conclusions Delayed rifampin absorption may be associated with elevated markers of bacterial translocation among HIV-infected individuals naïve to antiretroviral therapy. This trial is registered with NCT01845298.
Simulating Q-switched ytterbium-doped double clad fiber laser

We present a model for Q-switched, double cladding Yb-doped fiber laser. We investigate the effect of length of fiber and repetition rate of acousto-optic modulator on the duration and energy of the fiber laser pulse. Our modeling shows that by increasing of the fiber laser length the shape of pulse change and energy increase. And also by increasing the repetition rate frequency the energy of pulses decreases.
Causal effects of the microbiota on immune-mediated diseases

This Review summarizes current strategies for modeling host-microbiome interactions in the mammalian gastrointestinal tract. The mammalian immune system has evolved in the presence of a complex community of indigenous microorganisms that constitutively colonize all barrier surfaces. This intimate relationship has resulted in the development of a vast array of reciprocal interactions between the microbiota and the host immune system, particularly in the intestine, where the density and diversity of indigenous microbes are greatest. Alterations in the gut microbiota have been correlated with almost every known immunological disease, but in most cases, it remains unclear whether these changes are a cause or effect of the disease or merely a reflection of epidemiological differences between groups. Here, we review recent efforts to demonstrate a causal role for the microbiota in health and disease, outline experimental advances that have made these studies possible, and highlight how changes in microbial composition may influence immune system function.
Numerical Computation of Dynamic Character Coefficient of Journal Bearing

The purpose of this study is to determine the dynamic character coefficient of journal bearing with the consideration of bearing load direction and oil groove. Based on numerical differential method, the oil film pressure distribution on journal bearing is obtained with the point-by-point relaxation iteration method. Then, the dynamic characters are calculated by numerical integral algorithm.The calculation program is developed for the dynamic characteristics of journal bearing. The computation method provides a useful guide for the numerical simulation of rotary parts.
Temperature Distribution in Pocketed Thrust Washers

This article presents an experimental and numerical investigation of temperature distribution in a pocketed thrust washer. An experimental test rig was designed and developed to measure the temperature in the thrust washer contact under various operating conditions. To measure the temperature in the contact, a thin layer of thermochromic material was placed beneath the pocketed surface. The thermochromic material allowed temperature measurements across the contact through color contours displayed on the sheet. Video recording during operation showed the thermochromic sheet dynamically adapting to the rising temperature in the bearing. For the numerical investigation, the thermal Reynolds and energy equations were simultaneously solved subject to boundary condition to determine the pressure and temperature within the thrust washer. The thermal Reynolds equation was augmented with the Jacobsson-Floberg-Olsson (JFO) boundary condition to model cavitation and the energy equation was used to determine temperature and viscosity variations across the film. Experimental and numerical results showed significantly lower temperatures within the cavitation region due primarily to lower heat transfer from the gas to the solid. The temperature profile and corresponding operating conditions of the bearing obtained from the model correlated well with the experimental results.
Robust Relay Beamforming Against Jamming Attack

In this letter, we surpass the jamming effect and also estimate the jamming channel state information by using the Kalman filtering approach. Furthermore, we design a closed-form beamforming weight for maximizing the achievable rate subject to the condition that the total relays power transmission would be below a predefined threshold level, which is formulated as a quadratically constrained quadratic program. Simulation results show the efficient performance of the proposed method for different destruction powers of the jammer by achieving the Cramér–Rao lower bound.
Increased myocardial native T1 relaxation time in patients with nonischemic dilated cardiomyopathy with complex ventricular arrhythmia

To study the relationship between diffuse myocardial fibrosis and complex ventricular arrhythmias (ComVA) in patients with nonischemic dilated cardiomyopathy (NICM). We hypothesized that NICM patients with ComVA would have a higher native myocardial T1 time, suggesting more extensive myocardial diffuse fibrosis.
Axially vascularized tissue‐engineered bone constructs retain their in vivo angiogenic and osteogenic capacity after high‐dose irradiation

In order to introduce bone tissue engineering to the field of oncological reconstruction, we are investigating for the first time the effect of various doses of ionizing irradiation on axially vascularized bone constructs. Synthetic bone constructs were created and implanted in 32 Lewis rats. Each construct was axially vascularized through an arteriovenous loop made by direct anastomosis of the saphenous vessels. After 2 weeks, the animals received ionizing irradiation of 9 Gy, 12 Gy and 15 Gy, and were accordingly classified to groups I, II and III, respectively. Group IV was not irradiated and acted as a control. Tissue generation, vascularity, cellular proliferation and apoptosis were investigated either 2 or 5 weeks after irradiation through micro‐computed tomography, histomorphometry and real‐time polymerase chain reaction (PCR). At 2 weeks after irradiation, tissue generation and central vascularity were significantly lower and apoptosis was significantly higher in groups II and III than group IV, but without signs of necrosis. Cellular proliferation was significantly lower in groups I and II. After 5 weeks, the irradiated groups showed improvement in all parameters in relation to the control group, indicating a retained capacity for angiogenesis after irradiation. PCR results confirmed the expression of osteogenesis‐related genes in all irradiated groups. Dense collagen was detected 5 weeks after irradiation, and one construct showed discrete islands of bone indicating a retained osteogenic capacity after irradiation. This demonstrates for the first time that axial vascularization was capable of supporting a synthetic bone construct after a high dose of irradiation that is comparable to adjuvant radiotherapy. Copyright © 2016 John Wiley & Sons, Ltd.
A DECISION SUPPORT SYSTEM FOR SOIL PRODUCTIVITY AND EROSION IN POLK COUNTY , NEBRASKA

GIS-based decision-support systems are powerful, new tools for assessing inherent soil productivity and potential erosion. This study integrates digital soil survey (SSURGO) information, climate, LandSat TM-derived land cover, and 30m digital elevation data (NEDS) to spatially model regions of soil productivity and highly erodible lands in Polk County, Nebraska. The approach combines soil productivity indices, derived from the "Soil Ratings for Plant Growth" (SRPG), and land cover to identify poorer quality soil landscapes in corn and soybean production. Models using the Revised Universal Soil-Loss Equation test possible conservation strategies to reduce soil-loss in areas with high potential erosion rates. These decision support tools target conservation needs at both the county and farm scales and hold promise for federal and state agencies.
Recent Progress in Electronic Skin

The skin is the largest organ of the human body and can sense pressure, temperature, and other complex environmental stimuli or conditions. The mimicry of human skin's sensory ability via electronics is a topic of innovative research that could find broad applications in robotics, artificial intelligence, and human–machine interfaces, all of which promote the development of electronic skin (e‐skin). To imitate tactile sensing via e‐skins, flexible and stretchable pressure sensor arrays are constructed based on different transduction mechanisms and structural designs. These arrays can map pressure with high resolution and rapid response beyond that of human perception. Multi‐modal force sensing, temperature, and humidity detection, as well as self‐healing abilities are also exploited for multi‐functional e‐skins. Other recent progress in this field includes the integration with high‐density flexible circuits for signal processing, the combination with wireless technology for convenient sensing and energy/data transfer, and the development of self‐powered e‐skins. Future opportunities lie in the fabrication of highly intelligent e‐skins that can sense and respond to variations in the external environment. The rapidly increasing innovations in this area will be important to the scientific community and to the future of human life.