Miracle-dz/UniFAR-FTUs huggingface dataset:
Haemorrhagic toxin and lethal toxin from Clostridium sordellii strain vpi9048: molecular characterization and comparative analysis of substrate specificity of the large clostridial glucosylating toxins

Large clostridial glucosylating toxins (LCGTs) are produced by toxigenic strains of Clostridium difficile, Clostridium perfringens, Clostridium novyi and Clostridium sordellii. While most C. sordellii strains solely produce lethal toxin (TcsL), C. sordellii strain VPI9048 co‐produces both hemorrhagic toxin (TcsH) and TcsL. Here, the sequences of TcsH‐9048 and TcsL‐9048 are provided, showing that both toxins retain conserved LCGT features and that TcsL and TcsH are highly related to Toxin A (TcdA) and Toxin B (TcdB) from C. difficile strain VPI10463. The substrate profile of the toxins was investigated with recombinant LCGT transferase domains (rN) and a wide panel of small GTPases. rN‐TcsH‐9048 and rN‐TcdA‐10463 glucosylated preferably Rho‐GTPases but also Ras‐GTPases to some extent. In this respect, rN‐TcsH‐9048 and rN‐TcdA‐10463 differ from the respective full‐length TcsH‐9048 and TcdA‐10463, which exclusively glucosylate Rho‐GTPases. rN‐TcsL‐9048 and full length TcsL‐9048 glucosylate both Rho‐ and Ras‐GTPases, whereas rN‐TcdB‐10463 and full length TcdB‐10463 exclusively glucosylate Rho‐GTPases. Vero cells treated with full length TcsH‐9048 or TcdA‐10463 also showed glucosylation of Ras, albeit to a lower extent than of Rho‐GTPases. Thus, in vitro analysis of substrate spectra using recombinant transferase domains corresponding to the auto‐proteolytically cleaved domains, predicts more precisely the in vivo substrates than the full length toxins. Except for TcdB‐1470, all LCGTs evoked increased expression of the small GTPase RhoB, which exhibited cytoprotective activity in cells treated with TcsL isoforms, but pro‐apoptotic activity in cells treated with TcdA, TcdB, and TcsH. All LCGTs induced a rapid dephosphorylation of pY118‐paxillin and of pS144/141‐PAK1/2 prior to actin filament depolymerization indicating that disassembly of focal adhesions is an early event leading to the disorganization of the actin cytoskeleton.
‘Direct PCR’ optimization yields a rapid, cost‐effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction

Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction (‘direct PCR’) and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands.
Piezoelectric thin films: an integrated review of transducers and energy harvesting

Piezoelectric thin films offer a number of advantages in various applications, such as high energy density harvesters, a wide dynamic range, and high sensitivity sensors, as well as large displacement and low power consumption actuators. This review covers the available material forms and applications of piezoelectric thin films: lead zirconate titanate (PZT)-based thin films, lead-free piezoelectric thin films, piezopolymer films, cellulose-based electroactive paper (EAPap), and many other thin films used for electromechanical transduction. The electromechanical properties and performances of piezoelectric films are compared and their suitability for particular applications are reported. The key ideas of piezoelectric thin films are reviewed and discussed for sensory and actuation systems, energy harvesting, and medical and acoustic transducers. In the last section, an insight into the future outlook and possibilities for thin film-based devices and their integration into real-world applications is presented.
Cisplatin resistance conferred by the RAD51D (E233G) genetic variant is dependent upon p53 status in human breast carcinoma cell lines

RAD51D, a paralog of the mammalian RAD51 gene, contributes towards maintaining genomic integrity by homologous recombination DNA repair and telomere maintenance. A RAD51D variant, E233G, was initially identified as a potential susceptibility allele in high‐risk, site‐specific, familial breast cancer. We describe in this report that the Rad51d (E233G) genetic variant confers increased cisplatin resistance and cell growth phenotypes in human breast carcinoma cell lines with a mutant p53 gene (BT20 and T47D) but not with a wild‐type p53 gene (MCF‐7). Treatment with a p53 specific inhibitor, pifithrin α, restored this resistant phenotype in the MCF‐7 cell line. Additionally, Rad51d (E233G) conferred increased cisplatin resistance of an MCF7 cell line in which p53 expression was stably knocked down by shRNAp53, indicating that the effect of this variant is dependent upon p53 status. Further study of Rad51d (E233G) will provide mechanistic insight towards the role of RAD51D in cellular response to anticancer agents and as a potential target for cancer therapy. © 2009 Wiley‐Liss, Inc.
HYPERSENSITIVITY OF MELATONIN SUPPRESSION IN RESPONSE TO LIGHT IN PATIENTS WITH DELAYED SLEEP PHASE SYNDROME*

Patients with delayed sleep phase syndrome (DSPS) experiencea chronic mismatch between the usual daily schedule required by the individual'senvironment and their circadian sleep-wake pattern, resulting in major academic,work, and social problems. Although functional abnormalities of the circadianpacemaker system have been reported in patients with DSPS, the etiology ofDSPS has not been fully elucidated. One hypothesis proposed to explain whypatients with DSPS fail to synchronize their 24h sleep-wake cycle to theirenvironment is that they might have reduced sensitivity to environmental timecues, most notably light-dark cycles. Therefore, we compared the sensitivityof melatonin suppression in response to light in patients with DSPS and normalcontrol subjects. Fifteen patients with DSPS and age- and sex-matched healthycontrols were studied. As the melatonin secretion rhythm in patients withDSPS was expected to be delayed compared to the controls, the time of peakmelatonin secretion was determined in each subject in the first session. Inthe second session, each subject was exposed to light with an intensity of1000 lux for 2h beginning 2h prior to his or her peak melatonin secretion.Melatonin was measured by radioimmunoassay in saliva sampled every 30 minutesduring the period of light exposure. Suppression of the melatonin concentrationin saliva was dependent on duration of light exposure. In addition, the suppressiveeffect of light on the melatonin concentration was significantly greater inpatients with DSPS than in control subjects. The results suggest hypersensitivityto nighttime light exposure in patients with this syndrome. Our findings thereforesuggest that evening light restriction is important for preventing patientswith DSPS from developing a sleep phase delay. (ChronobiologyInternational, 18(2), 263–271, 2001)
Efficient point cloud collision detection and analysis in a tunnel environment using kinematic laser scanning and K-D Tree search

Abstract. Measuring the structure gauge of tunnels and other narrow passages has so far been the only way to evaluate whether large vehicles can pass through them. But especially for very long vehicles like train wagons and their cargo, the structure gauge is an insufficient measure because the center part of the vehicle between two bogies will inevitably leave the swept volume of its cross section when moving along any other trajectory than a straight line perpendicular to its cross section. In addition, the vehicle as well as the cargo must keep a minimum safety margin from the environment at all points of its trajectory. This paper explores an automated method to check for possible collisions of a model represented by a 3D point cloud moving through the 3D point cloud of an environment. We were given environment data of a train track through a narrow tunnel where simply relying on the structure gauge would indicate that a given wagon would pass through without any collision even though in reality, the train wagon would collide with the inner tunnel wall inside a sharp turn of the tracks. The k-d tree based collision detection method presented in this paper is able to correctly highlight these collisions and indicate the penetration depth of each colliding point of the environment into the model of the train wagon. It can be generalized for any setup where two static point clouds have to be tested for intersection along a trajectory.
Adaptive consensus algorithms for real‐time operation of multi‐agent systems affected by switching network events

We propose a control strategy based on distributed adaptive leader‐follower consensus algorithms for multi‐agent systems (MAS) affected by switching network events. The strategy allows each agent in the MAS to compute its own control input based on local information and information coming from its neighbors. In this sense, MAS distributed control laws are obtained where the coupling gain of the associated communication graph is adapted dynamically in real‐time. The consensus algorithm is extended with a switching network topology approach, which ensures appropriate performance even when the MAS network topology is prone to arbitrary switching. A real‐time experimental application is presented, where a MAS consisting of four rotorcraft UAS successfully performed the tasks of autonomously approaching and escorting a leader, even in the situation when the network topology was arbitrarily changing. Additionally, a Lyapunov stability analysis is included, which demonstrates that the tracking errors between leader and follower agents converge asymptotically to zero. Copyright © 2016 John Wiley & Sons, Ltd.
Water diffusion heterogeneity index in the human brain is insensitive to the orientation of applied magnetic field gradients

The α diffusion‐weighted imaging (DWI) method was developed to study heterogeneous water diffusion in the human brain using magnetic resonance imaging (MRI). An advantage of this model is that it does not require an assumption about the shape of the intravoxel distribution of apparent diffusion rates, and it has a calculable relationship to this distribution. The α‐DWI technique is useful for detecting microstructural tissue changes associated with brain tumor invasion, and may be useful for directing therapy to invading tumor cells. In previous work, α‐DWI was performed with magnetic field gradients applied along a single direction in order to avoid artificially introducing a source of heterogeneity to the decay. However, it is known that restricted diffusion is anisotropic in the brain, and the α‐DWI method must take this into account to be complete. In this work the relationship between the applied magnetic field gradients and the fitted stretched‐exponential model parameters was studied in the human brain. It was found the distributed diffusion coefficient (DDC) varies with the direction of applied gradients, while the heterogeneity index α is relatively direction‐insensitive. It is proposed that in clinical use, maps of α can be created using diffusion‐weighting gradients applied in a single direction that reflect the tissue heterogeneity. Magn Reson Med, 2006. Published 2006 Wiley‐Liss, Inc.
A feasibility study of trauma-sensitive obstetric care for low-income, ethno-racial minority pregnant abuse survivors

Abstract Purpose: This study evaluated the feasibility and acceptability of an integrated (psychological and obstetric) intervention for pregnant abuse survivors with posttraumatic stress symptoms (PTS) from low-income, ethno-racial minority backgrounds. Methods: Trauma-sensitive obstetrics to promote control, anxiety-reduction and empowerment (TO-CARE) offers cognitive-behavioral therapy (CBT) coping skills delivered over six sessions by therapists, coupled with trauma-sensitive obstetric care from specially-trained obstetric physicians. Results: Participants were 21 women who completed at least three sessions of CBT, totaling 51.2% of eligible participants. Participants received approximately one-third (M = 2.29; SD = 2.15) of their prenatal visits with obstetric residents trained in trauma-sensitive care. Nearly all participants (95%) reported that they benefited from the intervention. Although most participants demonstrated improvement in PTS, only four demonstrated reliable improvement, and two demonstrated reliable improvement in depression symptoms. These improvements appeared to be maintained at postpartum follow-up for two of the participants. Conclusions: Our findings suggest that TO-CARE was acceptable to pregnant abuse survivors and may be a promising intervention to reduce symptoms of distress. Implications of the low retention rate for the CBT (51.2%) are discussed in the context of interventions for low-income minority pregnant women. Limitations regarding feasibility of the integrated intervention are discussed.
T2 hyperintensity along the cortico‐spinal tract in cirrhosis relates to functional abnormalities

Magnetic resonance has shown T2 hyperintensity along the cortico‐spinal tract in the brain of cirrhotic patients. This abnormality, which is reversible after liver transplantation, appears to correspond to mild edema. Because astrocytic edema present in hepatic encephalopathy may be responsible for neuronal dysfunction, we studied whether T2 hyperintensity along the cortico‐spinal tract may relate to functional abnormalities. Twenty patients with cirrhosis underwent neuropsychologic tests, neurophysiologic study of the cortico‐spinal tract with transcranial magnetic stimulation, and 1H‐magnetic resonance. The study was repeated 6 months after liver transplantation (n = 15) and was compared with a control group of healthy subjects (n = 11). Cirrhotic patients exhibited increased T2 signal and several functional abnormalities along the cortico‐spinal tract (increased central motor conduction time, increased motor cortical threshold, and decreased motor‐evoked potential amplitude). Functional abnormalities reversed after liver transplantation and were associated with normalization of T2 cortico‐spinal hyperintensity and with improvement of minimal hepatic encephalopathy. In conclusion, T2 hyperintensity along the cortico‐spinal tract in cirrhosis relates to functional abnormalities that are reversible after liver transplantation. These findings suggest that mild cerebral edema along the cortico‐spinal pathway may cause neuronal dysfunction. These results support the participation of astrocytic edema in the pathogenesis of hepatic encephalopathy. (Hepatology 2003;38:1026–1033).
Transferrin receptor expression in normal skin and in various cutaneous tumors

In the majority of human cells the transferrin receptor (TFR) plays an important role by mediating the cellular iron uptake. The TFR is especially expressed by proliferating cells and has been found in high amounts in malignant tumors. The distribution of the TFR in frozen sections of 89 skin biopsies of normal skin and of various cutaneous tumors was investigated using an anti‐TFR monoclonal antibody (OKT9) and a 3‐step immunoperoxidase method. Our results indicate that in normal human skin the TFR shows a characteristic microanatomical distribution in the basal cell layer correlated to the architectural pattern of the dermal‐epidermal interface. In cutaneous lymphomas of high grade malignancy the TFR was expressed in virtually all cells compared to only 25–75% in low grade lymphomas. Malignant melanomas were strongly positive in the whole tumor tissue, whereas benign melanocytic nevi were largely negative. Obviously the immunohistochemical demonstration of the TFR may serve as prognostic indicator or diagnostic aid, respectively.
Sharks: Attraction by Low-Frequency Sounds

Large sharks (Carcharhinidae, Sphyrnidae), in their natural environment, were attracted to low-frequency (predominantly 20 to 60 cy/sec) pulsed sounds, but apparently not to higher frequency (400 to 600 cy/sec) pulsed sounds, or to low-frequency continuous sounds. The sharks apparently detected and oriented to the sounds in the acoustic far field.
EFFECT OF DENERVATION AND ENZYME INHIBITION ON DOPA DECARBOXYLASE AND MONOAMINE OXIDASE ACTIVITIES OF RAT PINEAL GLAND *

THE pineal gland of the rat contains large amounts of 5-HT (QUAY and HALEVY, 1962; BERTLER, FALCK and OWMAN, 1963; QUAY, 1963) which is located partly in the pineal parenchyma and partly in the pineal sympathetic nerves (BERTLER et al., 1963, 1964; OWMAN, 1964a). These are noradrenergic, but they take up and store also 5-HT (OWMAN, 1964a and b). The nerves supply the parenchymal cells of the gland and also enclose the intrapineal vessels (ARIENS KAPPERS, 1960; BERTLER et al., 1963). The present investigation deals with the activity of some enzymes involved in the metabolism of monoamines in the pineal gland. Some data are already available on hydroxyindole-0-methyl transferase, which is responsible for melatonin formation (AXELROD, MACLEAN, ALBERS and WEISSBACH, 1961 ; WURTMAN, AXELROD and PHILLIPS 1963; WURTMAN, AXELROD and FISCHER, 1964); a few studies on the monoamine oxidase activity have also been published (SMITH, 1963 ; WURTMAN et a]., 1963), but evidence on which to decide whether or not 5-HT is synthesized in the pineal parenchymal cells is still lacking. It is now generally accepted that the formation of 5-HT from 5-hydroxytryptophan is catalysed by an unspecific aromatic amino acid decarboxylase (WEISSBACH, LOVENBERG and UDENFRIEND 1960a, LOVENBERG, WEISSBACH and UDENFRIEND, 1962) identical with DOPA decarboxylase (ROSENGREN, 1960). In the present study the assumption was made that dopamine and 5-HT are produced by the same enzyme, DOPA decarboxylase. The technique used for the study of dopamine formation is the most sensitive method available. DOPA decarboxylase and M A 0 activities were studied in normal and denervated rat pineal glands; the possible significance of these enzymes in the metabolism of 5-HT in pineal nerves and parenchyma was also investigated by means of enzyme inhibitors. M A T E R I A L AND METHODS Experimental. Adult rats of both sexes were used. The histological and histochemical investigations included 207 animals; 550 animals were used for measurements of enzyme activities. The animals in the former experiments were killed by decapitation under light ether anaesthesia, those used in the latter section were killed, between 9 a.m. and 11 a.m. of the day of the experiment, by a blow on the neck. Some animals were submitted to bilateral cervical sympathectomy by removing both superior cervical ganglia under ether anaesthesia. The animals were killed by decapitation under ether anaesthesia at different stages after the operation.
Efficient SAT Approach to Multi-Agent Path Finding Under the Sum of Costs Objective

In the multi-agent path ﬁnding (MAPF) the task is to ﬁnd non-conﬂicting paths for multiple agents. In this paper we present the ﬁrst SAT-solver for the sum-of-costs variant of MAPF which was previously only solved by search-based methods. Using both a lower bound on the sum-of-costs and an upper bound on the makespan, we are able to have a reasonable number of variables in our SAT encoding. We then further improve the encoding by borrowing ideas from ICTS, a search-based solver. Experimental evaluation on several domains showed that there are many scenarios where the new SAT-based method outperforms the best variants of previous sum-of-costs search solvers - the ICTS and ICBS algorithms
Associations between Health-Related Physical Fitness, Academic Achievement and Selected Academic Behaviors of Elementary and Middle School Students in the State of Mississippi.

A wide variety of school-based physical activity contexts have been recently associated with various measures of academic performance. Of these studies, a small number employing objective measures of student fitness have identified a relationship with academic achievements. However, even among these studies, the fitness-academic link has not been conclusively recognized or regularly assessed with regards to academic behaviors and sociodemographic variables. The purpose of this study was to explore the relationships among these variables by using objective measures of fitness, standardized Language Arts and Math test scores, attendance records, discipline actions, and socio-demographic information from a sample of 2,992 Mississippi (USA) public school children in grades 3-8. The sample consisted of students who were mostly male (52.4%), white (52.3%), in grades 3-5 (64.2%), within a healthy weight range (54.1%), and qualified for free/reduced price lunch (63.7%). The results indicated a statistically significant positive correlation between fitness and standardized test scores in Language Arts and Math and a statistically significant negative relationship with school absences. The relationships remained significant while controlling for gender, race, and socioeconomic status. Given that students who were more fit had higher test scores and fewer absences, these findings warrant consideration in the educational policy making process.
Red blood cell fatty acids in multiple sclerosis

The fatty acid (FA) composition of each phospholipid constituent of the red blood cells (RBC) was analyzed, by thin‐layer and gas chromatography techniques, in 61 multiple sclerosis (MS) patients and 61 normal subjects, in whom the plasma lipid FA composition had previously been studied. The MS patients showed a significant decrease in the proportions of linoleic and arachidonic acids in most phospholipids, with a compensatory increase of saturated FA. Correlations between FA percentages in plasma and cell lipids demonstrated abnormalities in the MS patients, suggestive of a disturbance in the exchange between these compartments. The alterations reported in plasma and RBC in the MS patients are consistent with a relative deficiency of essential FA