Miracle-dz/UniFAR-FTUs huggingface dataset:
The Essential Transfer Protein TraM Binds to DNA as a Tetramer*

The TraM proteins encoded by F-like plasmids are sequence specific DNA binding proteins that are essential for conjugative DNA transfer. We investigated the quarternary structure and the DNA binding properties of the TraM wild-type protein of the resistance plasmid R1 and two mutant forms thereof. Size-exclusion chromatography and differential scanning calorimetry showed that purified TraM protein (amino acids 2–127) forms stable tetramers in solution. A truncated version of the protein termed TraMM26 (amino acids 2–56) forms dimers. Thus, the dimerization and tetramerization domains can be assigned to the N-terminal and C-terminal domains of TraM, respectively. Further analyses using chemical cross-linking and light scattering corroborated the preferentially tetrameric nature of the protein but also suggest that TraM has a tendency to form higher aggregates. Band-shift and fluorescence spectroscopy investigations of TraM-DNA complexes revealed that the TraM protein is also tetrameric when bound to its minimal DNA binding site. The deduced binding constant in the range of 108 m −1 demonstrated a very strong binding of TraM to its preferred DNA sequence. Secondary structure analysis based on CD measurements showed that TraM is mainly α-helical with a significant increase in α-helicity (48 to 58%) upon DNA-binding, indicating an induced fit mechanism.
The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901T Reveals a Broad Potential for Degradation of Algal Polysaccharides

ABSTRACT In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901T), an isolate from the green alga Acrosiphonia sonderi. F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.
Activities of superoxide dismutase and glutathione peroxidase in leaves of different cultivars of Liriope spicata L. on 10% SDS-PAGE gels

Activities of superoxide dismutase (SOD) and glutathione peroxidase (GPx) in leaf crude extracts of different cultivars (small leaf, SL, big leaf BL. thin leaf, TL) of Liriope spicata L. were detected on 10% SDS-PAGE gels. All cultivars contained different Cu/Zn SOD isozymes with molecular masses between 30 and 50 kDa, which were identified by inhibitor tests. They also contained different GPx isozymes with molecular masses between 50 and 64 kDa. It was found that SOD isozymes were stable during 40 to 65℃ treatment, however, no SOD activity could be detected at either 70 or 80℃ for 5 min. In contrast, all GPx isozymes were stable under 80℃ for 5 min, and GPx in SL and TL cultivars could resist 80℃ treatment for 30 min.
Probiotics as complementary therapy for hypercholesterolemia

The role of probiotic organisms as alternative or complementary therapy in combating large number of gastro intestinal disorders and their ability to enhance immune response attracts global attention. In addition, their therapeutic use towards cholesterol-lowering activities has further increased their applications as effective probiotics for humans as supplements in milk and yoghurt, since there are no other supplements for hypercholesterolemia, which is the crucial risk factor for cardiovascular diseases. Changes in dietary habits, stressful life and lack of physical activities are the precursors for increasing incidences of hypercholesterolemia and subsequently cardiovascular diseases. The present review focuses on some of the animal studies and clinical trials conducted with probiotic lactobacilli and bifidobacteria. This review may throw some light to prove the ability of these probiotics as a novel alternative or adjuvants to chemical drugs to help fight hypercholesterolemia.
Analysis, Design, and Control of Bidirectional Cascoded Configuration for a Fuel Cell Hybrid Power System

This paper presents a cascoded configuration combining a fuel cell (FC), a battery, and an ultracapacitor module (UCM) to create a hybrid power system. A cascoded configuration is constructed using a modified bidirectional flyback converter, which connects the battery and UCM in cascode to efficiently provide hybrid power. An active FC voltage control strategy is presented to manage the power flows of the proposed cascoded system. In this paper, the simulated hybrid power of the motion of an electric vehicle is illustrated in different situations. The experimental results show that the power flows using the proposed control strategy verify the theoretical analysis. In addition, the overall efficiency of the proposed hybrid power system at overload operation is much higher than the conventional one, and it can achieve 96%.
Antecedents for forming simultaneous alliances or one-by-one alliances

This article extends existing alliance portfolio studies by exploring differences of antecedents for forming simultaneous alliances and one-by-one alliances using data from 1,029 alliances in the global pharmaceutical industry. The research’s findings suggest that firms are inclined to form simultaneous alliances when they have more prior alliance experience, conduct exploration alliances, or are in high level of technological diversification. Second, although simultaneous alliance formation may decrease a firm’s performance, greater alliance experience and inter-industry alliances may mitigate such the negative effect of simultaneous alliance formation on firm performance. Low levels of technological diversification may increase firm performance as forming simultaneous alliances. Moreover, propensity to form simultaneous alliances is increased with the increased number of formed alliances as larger firm size, organizational experience, and alliance experience take place. This article contributes to the current strategic alliances and organizational learning literature by introducing the concept of simultaneous and one-by-one alliances.
Novel Diketopiperazine Enhances Motor and Cognitive Recovery after Traumatic Brain Injury in Rats and Shows Neuroprotection In Vitro and In Vivo

The authors developed a novel diketopiperazine that shows neuroprotective activity in a variety of in vitro models, as well as in a clinically relevant experimental model of traumatic brain injury (TBI) in rats. Treatment with 1-ARA-35b (35b), a cyclized dipeptide derived from a modified thyrotropin-releasing hormone (TRH) analog, significantly reduced cell death associated with necrosis (maitotoxin), apoptosis (staurosporine), or mechanical injury in neuronal–glial cocultures. Rats subjected to lateral fluid percussion–induced TBI and then treated with 1 mg/kg intravenous 35b thirty minutes after trauma showed significantly improved motor recovery and spatial learning compared with vehicle-treated controls. Treatment also significantly reduced lesion volumes as shown by magnetic resonance imaging, and decreased the number of TUNEL-positive neurons observed in ipsilateral hippocampus. Unlike TRH or traditional TRH analogs, 35b treatment did not change mean arterial pressure, body temperature, or thyroid-stimulating hormone release, and did not have analeptic activity. Moreover, in contrast to TRH or typical TRH analogs, 35b administration after TBI did not alter free-magnesium concentration or cellular bioenergetic state. Receptor-binding studies showed that 35b did not act with high affinity at 50 classical receptors, channels, or transporters. Thus, 35b shows none of the typical physiologic actions associated with TRH, but possesses neuroprotective actions in vivo and in vitro, and appears to attenuate both necrotic and apoptotic cell death.
Changing Law from Barrier to Facilitator of Opioid Overdose Prevention

Opioid overdose is the leading cause of accidental injury death in the United States, taking the lives of over 16,000 Americans every year. Many of those deaths are preventable through the timely provision of naloxone, a drug that reliably and effectively reverses opioid overdose. However, that drug is often not available where and when it is needed, due in large part to laws that pre-date the overdose epidemic. Preliminary evidence suggests that amending those laws to encourage the prescription and use of naloxone will reduce opioid overdose deaths, and a number of states have done so in the past several years. Since legal amendments designed to facilitate naloxone access have no documented negative effects, can be implemented at little or no cost, and have the potential to save both lives and resources, states that have not passed them may benefit from doing so.
Virtual Me: a virtual communication method that enables simultaneous multiple existence as an avatar and/or agents

The paper proposes a new communication method, called "Virtual Me", that enables a user to simultaneously participate in multiple events such as meetings or lectures as a virtual-metamorphosed avatar controlled by the user and/or as a computer-controlled autonomous agents. By interpreting non-verbal data generated by the other participants at each event, the system determines when to switch between using virtual metamorphosis or employing agents. We demonstrate the effectiveness of this method in a prototype of the Virtual Me system. It is the authors' hope that this technology may be in the interest not only of time efficiency but also of enriched human communication.
THE BIOLOGICAL RESTORATION OF CENTRAL NERVOUS SYSTEM ARCHITECTURE AND FUNCTION: PART 1—FOUNDATIONS AND HISTORICAL LANDMARKS IN CONTEMPORARY STEM CELL BIOLOGY

SINCE THEIR DISCOVERY, stem cells have fascinated scientists with their ultimate potential: the ability to cure disease, repair altered physiology, and reverse neurological deficit. Stem cell science unquestionably promises to eliminate many of the tragic limitations contemporary medicine must acknowledge, and cloning may provide young cells for an aging population. Although it is widely believed that stem cells will transform the way medicine is practiced, therapeutic interventions using stem cell technology are still in their infancy. The 3 most common stem cell sources studied today are umbilical cord blood, bone marrow, and human embryos. Although cord blood is currently used to treat dozens of disorders and bone marrow stem cells have been used clinically since the 1960s, human embryonic stem cells have yet to be successfully applied to any disease. Undeniably, stem cell therapy has the potential to be one of the most powerful therapeutic options available. In this introductory article of a 5-part series on stem cells, we narrate the evolution of modern stem cell science, delineating major landmarks that will prove responsible for taking stem cell technology from the laboratory into revolutionary clinical applications: from the first milestone of identifying the mouse hematopoietic stem cell to the latest feats of producing pluripotent stem cells without embryos at all. In Part 2, we present the evidence demonstrating the certainty of adult mammalian neurogenesis; in Parts 3 and 4, we describe neurosurgical applications of stem cell technology; and in Part 5, we discuss the philosophical and ethical issues surrounding stem cell therapy, as well as future areas of exploration.
Deep Language: a comprehensive deep learning approach to end-to-end language recognition

This work explores the use of various Deep Neural Network (DNN) architectures for an end-to-end language identiﬁcation (LID) task. The approach has been proven to signiﬁcantly improve the state-of-art in many domains include speech recognition, computer vision and genomics. As an end-to-end system, deep learning removes the burden of hand crafting the feature extraction is conventional approach in LID. This versatility is achieved by training a very deep network to learn distributed representations of speech features with multiple levels of ab-straction. In this paper, we show that an end-to-end deep learning system can be used to recognize language from speech utterances with various lengths. Our results show that a combination of three deep architectures: feed-forward network, convolutional network and recurrent network can achieve the best performance compared to other network designs. Addition-ally, we compare our network performance to state-of-the-art BNF-based i-vector system on NIST 2015 Language Recognition Evaluation corpus. Key to our approach is that we effectively address computational and regularization issues into the network structure to build deeper architecture compare to any previous DNN approaches to language recognition task.
An in situ hybridization study of Runx2, Osterix, and Sox9 in the anlagen of mouse mandibular condylar cartilage in the early stages of embryogenesis

Mandibular condylar cartilage is the best‐studied mammalian secondary cartilage, differing from primary cartilage in that it originates from alkaline phosphatase‐positive progenitor cells. We previously demonstrated that three transcription factors related to bone and cartilage formation, namely Runx2, Osterix and Sox9, are simultaneously expressed in the anlage of mandibular condylar cartilage (condylar anlage) at embryonic day (E)14. In this study, expression of these transcription factors was investigated in the anlagen of mandibular bone (mandibular anlagen) from E11.0 to 14.0. Runx2 mRNA was first expressed in the mandibular anlage at E11.5. Osterix mRNA was first expressed at E12.0, and showed a different expression pattern from that of Runx2 from E12.5 to E14.0, confirming that Osterix acts downstream of Runx2. Sox9 mRNA was expressed in Meckel's cartilage and its anlagen throughout the experimental period, but not clearly in the mandibular anlagen until E13.0. At E13.5, the condylar anlage was morphologically identified at the posterior end of the mandibular anlage, and enhanced Sox9 mRNA expression was detected here. At this stage, Runx2 and Osterix mRNA were simultaneously detected in the condylar anlage. These results indicate that the Sox9 mRNA‐expressing condylar anlage is derived from Runx2/Osterix mRNA‐expressing mandibular anlage, and that upregulation of Sox9 in this region acts as a trigger for subsequent condylar cartilage formation.
Effect of short-term regression of atherosclerosis on reactivity of carotid and retinal arteries.

BACKGROUND AND PURPOSE This study tested the hypothesis that functional abnormalities of carotid and ocular arteries may improve after short-term regression of atherosclerosis, before regression of structural abnormalities. METHODS We examined effects of short-term dietary treatment of atherosclerosis on carotid and ocular vascular responses to serotonin and to platelet activation by collagen in vivo. Three groups of monkeys were studied: normal cynomolgus monkeys, monkeys fed an atherogenic diet for 34 months, and atherosclerotic monkeys that were fed a regression diet for 8.6 +/- 1.1 months (mean +/- SE). We measured changes in carotid blood flow (using a Doppler probe), retinal blood flow (using microspheres), and diameter of the internal carotid artery (using quantitative angiography). Endothelium-dependent relaxation to acetylcholine was studied in rings of internal carotid artery in vitro. RESULTS Carotid blood flow increased in response to both serotonin and collagen in normal monkeys, decreased in response to both agents in atherosclerotic monkeys, and was restored toward normal after regression. Serotonin had little effect on retinal blood flow in normal monkeys and produced a marked decrease in retinal blood flow in atherosclerotic monkeys; the vasoconstrictor response to serotonin was reduced after regression. Activation of platelets by collagen increased blood flow in normal monkeys, decreased blood flow in atherosclerotic monkeys, and had little effect after regression. Alterations in responses of the internal carotid artery were consistent with changes in carotid and ocular blood flow. Endothelium-dependent relaxation in vitro was impaired by atherosclerosis and was restored toward normal by regression. There was no reduction in intimal area of the atherosclerotic lesion in common carotid and ophthalmic arteries from regression monkeys, despite a marked reduction in cholesteryl ester. CONCLUSIONS Within a few months of regression of atherosclerosis, endothelial function and hyperresponsiveness of carotid and ocular arteries to serotonin and platelet activation return toward normal. Functional improvement is associated with resorption of lipid from atherosclerotic lesions, but with little reduction in size of intimal lesions.
Predicting the Risk of Rupture of Abdominal Aortic Aneurysms by Utilizing Various Geometrical Parameters: Revisiting the Diameter Criterion

The authors estimated noninvasively the wall stress distribution for actual abdominal aortic aneurysms (AAAs) in vivo on a patient-to-patient basis and correlated the peak wall stress (PWS) with various geometrical parameters. They studied 39 patients (37 men, mean age 73.7 ± 8.2 years) with an intact AAA (mean diameter 6.3 ± 1.7 cm) undergoing preoperative evaluation with spiral computed tomography (CT). Real 3-dimensional AAA geometry was obtained from image processing. Wall stress was determined by using a finite-element analysis. The aorta was considered isotropic with linear material properties and was loaded with a static pressure of 120.0 mm Hg. Various geometrical parameters were used to characterize the AAAs. PWS and each of the geometrical characteristics were correlated by use of Pearson's rank correlation coefficients. PWS varied from 10.2 to 65.8 N/cm2 (mean value 37.1 ± 9.9 N/cm2). Among the geometrical parameters, the PWS was well correlated with the mean centerline curvature, the maximum centerline curvature, and the maximum centerline torsion of the AAAs. The correlation of PWS with maximum diameter was nonsignificant. Multiple regression analysis revealed that the mean centerline curvature of the AAA was the only significant predictor of PWS and subsequent rupture risk. This noninvasive computational approach showed that geometrical parameters other than the maximum diameter are better indicators of AAA rupture.
Public Exposure from Indoor Radiofrequency Radiation in the City of Hebron, West Bank—Palestine

AbstractThis work presents the results of measured indoor exposure levels to radiofrequency (RF) radiation emitting sources in one of the major cities in the West Bank—the city of Hebron. Investigated RF emitters include FM, TV broadcasting stations, mobile telephony base stations, cordless phones [Digital Enhanced Cordless Telecommunications (DECT)], and wireless local area networks (WLAN). Measurements of power density were conducted in 343 locations representing different site categories in the city. The maximum total power density found at any location was about 2.3 × 10−2 W m−2 with a corresponding exposure quotient of about 0.01. This value is well below unity, indicating compliance with the guidelines of the International Commission on Non-ionizing Radiation Protection (ICNIRP). The average total exposure from all RF sources was 0.08 × 10−2 W m−2. The relative contributions from different sources to the total exposure in terms of exposure quotient were evaluated and found to be 46% from FM radio, 26% from GSM900, 15% from DECT phones, 9% from WLAN, 3% from unknown sources, and 1% from TV broadcasting. RF sources located outdoors contribute about 73% to the population exposure indoors.
Nonencapsulated Trichinella pseudospiralis Infection Impairs Follicular Helper T Cell Differentiation with Subclass-Selective Decreases in Antibody Responses

ABSTRACT Infectious microorganisms often modify host immunity to escape from immune elimination. Trichinella is a unique nematode of the helminth family, whose members parasitize the muscle cells inside the host without robust eliminative reactions. There are several species of Trichinella; some develop in muscle cells that become encapsulated (e.g., Trichinella spiralis) and others in cells that do not encapsulate (e.g., Trichinella pseudospiralis). It has already been established that Trichinella infection affects host immune responses in several experimental immune diseases in animal models; however, most of those studies were done using T. spiralis infection. As host immune responses to T. spiralis and T. pseudospiralis infections have been reported to be different, it is necessary to clarify how T. pseudospiralis infection influences the host immune responses. In this study, we investigated the influence on host humoral immunity in T. pseudospiralis-infected mice. We demonstrated that T. pseudospiralis infection decreased antigen-specific IgG2a and IgG2b antibody (Ab) production in mice immunized with a model antigen. This selective decrease in gamma interferon (IFN-γ)-dependent Ab production was not due to a decrease in IFN-γ production, and we instead found impaired follicular helper T (Tfh) cell differentiation. The affinity maturation of antigen-specific Ab tended to be delayed but was not significant in T. pseudospiralis-infected mice. We also observed that CD11b+ spleen cells in T. pseudospiralis-infected mice expressed CD206 and PD-L2, the phenotype of which was M2 macrophages with weak production of interleukin-6 (IL-6), possibly resulting in impaired Tfh differentiation. Taken together, our results indicate that nonencapsulated Trichinella infection induces selective dampening in humoral immunity with the suppression of Tfh differentiation.
Primary Practice of Green Mine Construction in Limestone Mine

Overall project of geologic environment comprehend- sive harnessing and landscape rehabilitation is put forward in production practice of Tangshan Sanyou Mine Corporation by using systems engineering process. Instructive research on building "Green Mine" demonstration plot in Hebei Province is realized in construction project which give attention to economic benefit of the mine and environmental factors. Linear programming is built for comprehensive utilization of waste rock in the orebody roof. And brief arts and crafts plan of waste dump ground reclamation is given.