Miracle-dz/UniFAR-FTUs huggingface dataset:
New tuberculosis drug development: targeting the shikimate pathway

Background: Tuberculosis (TB) remains a leading cause of morbidity and mortality worldwide, yet no new drugs have been developed in the last 40 years. Objective: The exceedingly lengthy TB chemotherapy and the increasing emergence of drug resistance complicated by HIV co-infection call for the development of new TB drugs. These problems are further compounded by a poor understanding of the biology of persister bacteria. Methods: New molecular tools have offered insights into potential new drug targets, particularly the enzymes of the shikimate pathway, which is the focus of this review. Results/conclusion: Shikimate pathway enzymes, especially shikimate kinase, may offer attractive targets for new TB drug and vaccine development.
Retrieval and reconsolidation: toward a neurobiology of remembering.

Memory lends itself to study through its retrieval whether it is evaluated by the behavior of a mouse in a swimming pool, a verbal report from a human subject, or inferred from an electrophysiological event. As William James so aptly pointed out, “the only proof of there being retention is that recall actually takes place. ” (1892). Such a view of memory as remembering is well elaborated in the theoretical reflections of Bergson (1896), in the seminal studies of Bartlett (1932) and later in those of Tulving (Tulving and Thomson 1973) and Craik (1983), who argue, after Bergson, that remembering is an activity similar to perceiving, in the sense that it involves the apprehension and comprehension of contemporary stimuli in the light of past experience. Although some memory retrieval is likely to occur spontaneously as a result of random fluctuations of patterns of neuronal activity, retrieval is usually brought about as a result of integration of incoming environmental information with the “memory network” driven by that information (Tulving and Thomson 1973). It follows from this that retrieval will lead to the formation of new memories made on the background of a retrieved prior experience. Therefore, it is inconceivable that new memory can be acquired independently of retrieval of past experience, in that it is memory of the past, that organizes and provides meaning to the present perceptual experience. Borrowing Tulving’s terminology, new episodic memory, to be remembered in a meaningful way, must be consolidated within a preexisting semantic memory. This analysis does not draw a clear demarcation between consolidation and retrieval processes and in this view, it can be assumed that every retrieval operation should trigger a reconsolidation process (Spear and Mueller 1984). Moreover, decoding or retrieval will change the information content of the “trace” such that memory can be viewed from a neurobiological point of view as an emergent, dynamic, adaptive property of the nervous system. The theoretical emphasis on memory reactivation and reconsolidation made here raises the issue, as yet ill addressed by neurobiological experiments, of factors that control or modulate these processes. We first review the literature dealing with the neurobiological factors that are involved in the actual retrieval process, a literature that was, until recently, relatively sparse. The advent of noninvasive imaging technology applicable to human studies has, however, awakened interest in this topic and has resulted in a proliferation of studies directly dealing with this aspect of memory function. These will be briefly discussed. The second part of this review deals with recent neurobiological evidence for reconsolidation of memories after their reactivation.
Routinely collected English birth data sets: comparisons and recommendations for reproductive epidemiology

Background In England there are four national routinely collected data sets on births: Office for National Statistics (ONS) births based on birth registrations; Hospital Episode Statistics (HES) deliveries (mothers’ information); HES births (babies’ information); and NHS Numbers for Babies (NN4B) based on ONS births plus gestational age and ethnicity information. This study describes and compares these data, with the aim of recommending the most appropriate data set(s) for use in epidemiological research and surveillance. Methods We assessed the completeness and quality of the data sets in relation to use in epidemiological research and surveillance and produced detailed descriptive statistics on common reproductive outcomes for each data set including temporal and spatial trends. Results ONS births is a high quality complete data set but lacks interpretive and clinical information. HES deliveries showed good agreement with ONS births but HES births showed larger amounts of missing or unavailable data. Both HES data sets had improved quality from 2003 onwards, but showed some local spatial variability. NN4B showed excellent agreement with ONS and HES deliveries for the years available (2006–2010). Annual number of births increased by 17.6% comparing 2002 with 2010 (ONS births). Approximately 6% of births were of low birth weight (2.6% term low birth weight) and 0.5% were stillbirths. Conclusions Routinely collected data on births provide a valuable resource for researchers. ONS and NN4B offer the most complete and accurate record of births. Where more detailed clinical information is required, HES deliveries offers a high quality data set that captures the majority of English births.
The Diagnosis of Spinal Dural Arteriovenous Fistulas

Study Design. Retrospective consecutive case series. Objective. To review and analyze clinical presentations and radiological imaging of 326 consecutive patients with spinal dural arteriovenous fistula (SDAVF) from 2 institutions. Summary of Background Data. The clinical presentations of SDAVF are nonspecific. Patients may be initially diagnosed with other spinal diseases. Magnetic resonance imaging (MRI) can reveal spinal cord changes associated with the disorder, but neurosurgeons often overlook these changes. Methods. From 1989 to 2009, 326 patients were diagnosed with SDAVF and treated at Qilu Hospital of Shandong University and the Xuanwu Hospital of the Capital University of Medical Sciences. We retrospectively reviewed the clinical records and radiological images of all patients, and collected and analyzed the related data. Results. Two hundred eighty-two males and 44 females (male/female ratio 6.4:1; mean age, 53.9 yr; SD, 12.1) were included in the study. Fistulas were located at the T7 spinal segment (41, 12.6%), but were more typically found at T5 to L5 (273, 82.5%). The most common initial symptoms were lower extremity weakness (234, 71.8%), sensory disturbance (229, 70.2%), and sphincter disturbance (87, 26.7%). These percentages increased to, 85.6%, 80.8%, and 52.5%, respectively, until patients were properly diagnosed. The mean diagnostic time to SDAVF was 19.9 months (SD, 25.2). Two major changes noted on magnetic resonance images were intramedullary T2-weighted signal hyperintensity (284, 87.1%) and perimedullary dilated vessels (251, 77%). Fistulas were often located outside of the vertebral segments of T2-weighted signal change (P = 0.005). Magnetic resonance angiography and computed tomography angiography of 33 (71.7%) patients revealed perimedullary dilated vessels and precisely located fistulas in 19 (41.3%) patients. Magnetic resonance angiography and computed tomography angiography studies of the perimedullary vessels also led to identification of a second fistula through angiography. Degenerative disc disease and myelitis were the most common misdiagnoses, and the patients were often treated incorrectly. Conclusion. “Worsening” and “symptoms combination” are progression characteristics of SDAVF. Patients should undergo spinal magnetic resonance imaging when they are first suspected to have SDAVF. Magnetic resonance angiography and computed tomography angiography as noninvasive angiography are helpful for diagnosis. Level of Evidence: 4
280 GHz tunable waveguide bandpass filter with MEMS tuning elements

This paper presents a novel tunable waveguide bandpass filter by using microelectromechanical (MEMS) technology. The movable element driven by the U-shape electrothermal microactuator can perturb the electromagnetic distribution of the resonator and change its resonance frequency. The designed three-pole tunable rectangular waveguide bandpass filter using three tuning elements operating at 279.4 GHz achieves a tuning range about 3.6 GHz, with the insert loss less than 1 dB.
Ginger Does Not Prevent Postoperative Nausea and Vomiting After Laparoscopic Surgery

IMPLICATIONS The potential antiemetic effect of two different oral doses of the herbal remedy ginger (Zingiber officinale) to prevent postoperative nausea and vomiting in 180 patients undergoing gynecologic laparoscopy was investigated in this randomized, double-blinded trial. Ginger failed to reduce the incidence of postoperative nausea and vomiting after these procedures.
Laser operation of a bulk Tm3+: Germanate glass laser around 2 µm with 50 % internal slope efficiency

In this report we have presented a spectroscopic and CW laser characterization of an efficient thulium doped GPNG bulk germanate glass pumped at 792 nm by Ti: Sapphire radiation. Laser characterization gave a maximum slope efficiency of 50 % comparable to the crystalline counterparts and we believe, to the best of our knowledge, this being the best for Tm-doped bulk glass lasers. The maximum output power was of 190 mW with a 4 % OC for -500 mW of absorbed power. In this report we can confirm that Germanate glass proved a good host for 2 mum Tnr+ lasers as suggested by G. Turri et al.[9]. Given that Germanate materials possess nonlinear refractive indexes around ~ 40 x 10"16 cm2/W [10] (approximately one order of magnitude higher that the ~ 3 x 10"16 cm2/W of the Ti:Sapphire[ll]) yielding pronounced Kerr lens susceptibilities, when combined with their broad tunability further suggests that they have good potential for ultrashort pulse operation.
Sequentially balanced three-squares cross-over designs.

Many cross-over designs with t > or = 2 treatments and periods and n = bt subjects (b an integer > or = 1) which incorporate balance for first-order carry-over effects are already known: single squares with any even value of t and some odd ones also; and sequentially balanced pairs of squares for any odd t > or = 3. We describe the construction of designs with b = 3, for t < or = 5, 7, 9, . This permits use of sequentially balanced designs for any combination of b > 1 and t, except for b = t = 3, for which no such design exists.
Trypan Blue Exclusion Test of Cell Viability

The protocol described in this appendix allows for light microscopic quantitation of cell viability. Cells are suspended in PBS containing trypan blue and then examined to determine the percentage of cells that have clear cytoplasm (viable cells) versus cells that have blue cytoplasm (nonviable cells). © 2015 by John Wiley & Sons, Inc.
Intrusion detection for Adhoc networks in IOT

IoT leads to the vision of connected world of physical and virtual processes, services and objects which are capable of providing a way on how to link them to internet. IoT is a major part of future internet that mainly integrates and enables numerous communication solutions and technologies and therefore, it is a notable interest to define how standard communication protocols could support the vision of IoT. In this context we present a comparative analysis on networks based on Ad Hoc On-Demand Distance Vector (AODV) network under various attacks like skin hole, black hole and worm hole.
Feasibility study of a unilateral RF array coil for MR-scintimammography

Despite its high sensitivity, the variable specificity of magnetic resonance imaging (MRI) in breast cancer diagnosis can lead to unnecessary biopsies and over-treatment. Scintimammography (SMM) could potentially supplement MRI to improve the diagnostic specificity. The synergistic combination of MRI and SMM (MRSMM) could result in both high sensitivity from MRI and high specificity from SMM. Development of such a dual-modality system requires the integration of a radio frequency (RF) coil and radiation detector in a strong magnetic field without significant mutual interference. In this study, we developed and tested a unilateral breast array coil specialized for MRSMM imaging. The electromagnetic field, specific absorption ratio and RF coil parameters with cadmium-zinc-telluride detectors encapsulated in specialized RF and gamma-ray shielding mounted within the RF coil were investigated through simulation and experimental measurements. Simultaneous MR and SMM images of a breast phantom were also acquired using the integrated MRSMM system. This work, we feel, represents an important step toward the fabrication of a working MRSMM system.
Genotype-phenotype analysis of CYP2C19 in the Tibetan population and its potential clinical implications in drug therapy

Cytochrome P450 2C19 (CYP2C19) is a highly polymorphic gene, it codes for a protein responsible for the metabolism of multiple clinically important therapeutic agents. However, there is currently no available data on the distribution of CYP2C19 mutant alleles in the Tibetan population. The aim of the present study was to identify different CYP2C19 mutant alleles and determine their frequencies, along with genotypic frequencies, in the Tibetan population. The whole CYP2C19 gene was amplified and sequenced in 96 unrelated, healthy Tibetans from the Tibet Autonomous Region of China, the promoter region, exons, introns and the 3′-UTR were screened for genetic variants. Three novel genetic polymorphisms in CYP2C19 were detected among a total of 27 different mutations. The allele frequencies of CYP2C19*1A, *1B, *2A, *3A and *17 were 50, 28.13, 15.10, 5.21 and 1.56%, respectively. The most common genotype combinations were CYP2C19*1A/*1B (56.25%) and *1A/*2A (30.21%). One novel non-synonymous mutation (Asn to Lys) in CYP2C19 was identified, and this mutation was predicted to be intolerant and benign by SIFT and PolyPhen-2, respectively. The observations of the present study may have important clinical implications for the use of medications metabolized by CYP2C19 among Tibetans.
Adult female acne: a new paradigm

In the adult female, acne is a chronic condition with a substantial negative psychological, social and emotional impact. Based on time of onset, two subtypes of adult female acne are recognized: ‘persistent acne’ is a continuation of the disease from adolescence, while ‘late‐onset acne’ first presents in adulthood. The morphological characteristics of adult female acne are often distinct from adolescent acne. In adults, inflammatory lesions (particularly papules, pustules and nodules) are generally more prominent on the lower chin, jawline and neck, and comedones are more often closed comedones (micro cysts). Adult acne is mainly mild‐to‐moderate in severity and may be refractory to treatment. A holistic approach to acne therapy should be taken in adult females, which combines standard treatments with adjunctive therapy and cosmetic use. A number of factors specific to the adult female influence choice of treatment, including the predisposition of older skin to irritation, a possible slow response to treatment, a high likelihood of good adherence, whether of child‐bearing age, and the psychosocial impact of the disease. Adherence to therapy should be encouraged through further patient education and a simplified regimen that is tailored to suit the individual patient’s needs and lifestyle. This article reviews the specific characteristics of adult female acne, and provides recommendations for acne therapy in this patient group.
It Does Take a Village

Family characteristics influence children's behavioral development, but so do variations in schools, neighborhoods, and communities. We documented extrafamilial environmental effects by fitting maximum likelihood models to questionnaire data collected from double dyads consisting of twins and their classmate controls. The classmate controls in each double dyad were genetic strangers living in separate households, but they shared school, neighborhood, and community environments with their yoked twin pair and with one another. At ages 11 to 12, the control classmates showed significant similarities in religious practices and smoking and drinking patterns, demonstrating that environmental influences outside the family affect children's behavioral development. Familial self-selection of residential neighborhoods may have contributed to these results, but direct effects of variation across communities, neighborhoods, and schools cannot be dismissed, and such effects warrant further study.
Integrating 3D Channel Model and Grid of Beams for 5G mMIMO System Level Simulations

Massive MIMO (mMIMO) antenna array and Grid of Beams (GoB) are one of the key components for 5G to achieve high spectral efficiency and coverage. System level simulations are necessary to optimally intergrate the components of 5G system. Simulations with mMIMO antenna array involve handling large matrices, which results in increased simulation time typically upto several days depending on the size of the antenna array. However, GoB are fixed wideband beams and the receiver sees only the effective channel which is a combination of the channel and the GoB. Therefore, for system level simulations it is sufficient to general only the effective channel. In this paper, we propose a simulation model to directly generate the effective channel based on the 3GPP 3D channel model. It is shown that for the simulation of urban macro cells scenario specified in TR 38.913, the computational effort can be reduced by a factor of 1000. Furthermore, simulations show that very high SINR and user throughput values are achievable through GoB.
Multiple psychotropic medication use for youths: a two-state comparison.

OBJECTIVE The aim of this study was to compare multiple psychotropic use among youths enrolled in two U.S. mid-Atlantic state Medicaid and state Children's Health Insurance Programs (SCHIP). METHODS Administrative data were used to examine multiple psychotropic use among youths less than 20 years of age and who were continuously enrolled in Medicaid or SCHIP programs in two states during 1999. Multiple psychotropic use referred to multiclass combinations and was defined by the number of months of multiple use. Main outcome measures were the prevalence of multiple psychotropic use and months of multiple use. Demographic and clinical characteristics, mental health visits, and common combinations were examined according to months of multiple use. RESULTS Among continuously enrolled youths, 21%-22% had at least one mental health-related visit, 8%-10% received a psychotropic medication, and 2%-3% received multiple psychotropic medications. Nearly one third (28%-30%) of youths with any psychotropic use received multiple medications, of which almost half was for 5-12 months. Multiclass use was more common in male, white, aged 10-14, disabled, and foster-care youths. Stimulants with antidepressants, antipsychotics, or alpha-agonists were the most common combinations. CONCLUSIONS Multiple use occurred in nearly one third of youths with any psychotropic treatment. Additional research is needed to investigate switching patterns and the effectiveness of combined pharmacotherapy.
Multi‐GPU algorithm for k‐nearest neighbor problem

The recommendation system is a mechanism which automatically recommends items that are likely to be of interest to the user. In the recommendation system, customers' preferences are encoded into vectors, and finding the nearest vectors to each vector is an essential part. This vector‐searching part of the problem is called a k‐nearest neighbor problem. We give an effective algorithm to solve this problem on multiple graphics processor units (GPUs). Our algorithm consists of two parts: the N‐body problem and the partial sort. For an algorithm of the N‐body problem, we applied the idea of a known algorithm, although another trick is needed to overcome the problem of small‐sized shared memory. For the partial sort, we give a novel GPU algorithm which is effective for small k. In our partial sort algorithm, a heap is accessed in parallel by threads with a low cost of synchronization. We show through an experiment that when the size of the problem is large, an implementation of the algorithm on two GPUs runs more than 330 times faster than a single core implementation on a latest CPU. Copyright © 2011 John Wiley & Sons, Ltd.
Mismatch DNA recognition protein from an extremely thermophilic bacterium, Thermus thermophilus HB8.

The mutS gene, implicated in DNA mismatch repair, was cloned from an extremely thermophilic bacterium, Thermus thermophilus HB8. Its nucleotide sequence encoded a 819-amino acid protein with a molecular mass of 91.4 kDa. Its predicted amino acid sequence showed 56 and 39% homology with Escherichia coli MutS and human hMsh2 proteins, respectively. The T.thermophilus mutS gene complemented the hypermutability of the E.coli mutS mutant, suggesting that T.thermophilus MutS protein was active in E.coli and could interact with E.coli MutL and/or MutH proteins. The T.thermophilus mutS gene product was overproduced in E.coli and then purified to homogeneity. Its molecular mass was estimated to be 91 kDa by SDS-PAGE but approx. 330 kDa by size-exclusion chromatography, suggesting that T.thermophilus MutS protein was a tetramer in its native state. Circular dichroic measurements indicated that this protein had an alpha-helical content of approx. 50%, and that it was stable between pH 1.5 and 12 at 25 degree C and was stable up to 80 degree C at neutral pH. Thermus thermophilus MutS protein hydrolyzed ATP to ADP and Pi, and its activity was maximal at 80 degrees C. The kinetic parameters of the ATPase activity at 65 degrees C were Km = 130 microM and Kcat = 0.11 s(-1). Thermus thermophilus MutS protein bound specifically with G-T mismatched DNA even at 60 degrees C.
A Framework for Protecting EJB Applications from Malicious Components

Enterprise JavaBeans (EJB) components in an EJB application can be obtained from various sources. These components may be in-house developed or bought from other vendors. In the latter case, the source code of the components is usually not available to application developers. The result is that the application may contain malicious components. We propose a framework called BFSec that protects EJB applications from vicious components. The framework examines bean methods invoked by each thread in applications and compares them with pre-defined business functions to check whether the latest calls of threads are proper. Unexpected calls, which are considered to be made by malicious components, will be blocked.
Intermittent chaos in Hamiltonian systems: The three-dimensional hydrogen atom in magnetic fields.

The trajectories of the highly excited hydrogen atom with nonvanishing pseudomomentum K are investigated. As a characteristic feature, we observe the intermittent behavior of the internal as well as of the center-of-mass motions which consist of alternating phases of strongly chaotic and quasiregular motion. During these phases, interesting physical phenomena appear. These phenomena as well as the intermittent behavior of the trajectories can be explained by the observation that, due to the finite nuclear mass, an additional confining potential appears. This confining potential has strong impact on the ionization of the hydrogen atom in general. We also investigate the correlation between the values of the internal angular momentum ${\mathit{L}}_{\mathit{z}}$ and the internal coordinate \ensuremath{\rho}. In fact, we are able to control intermittency by choosing different values of the energy, pseudomomentum, and magnetic-field strength.