Miracle-dz/UniFAR-FTUs huggingface dataset:
Concentration and Localization of Coexpressed ELAV/Hu Proteins Control Specificity of mRNA Processing

ABSTRACT Neuronally coexpressed ELAV/Hu proteins comprise a family of highly related RNA binding proteins which bind to very similar cognate sequences. How this redundancy is linked to in vivo function and how gene-specific regulation is achieved have not been clear. Analysis of mutants in Drosophila ELAV/Hu family proteins ELAV, FNE, and RBP9 and of genetic interactions among them indicates that they have mostly independent roles in neuronal development and function but have converging roles in the regulation of synaptic plasticity. Conversely, ELAV, FNE, RBP9, and human HuR bind ELAV target RNA in vitro with similar affinities. Likewise, all can regulate alternative splicing of ELAV target genes in nonneuronal wing disc cells and substitute for ELAV in eye development upon artificially increased expression; they can also substantially restore ELAV's biological functions when expressed under the control of the elav gene. Furthermore, ELAV-related Sex-lethal can regulate ELAV targets, and ELAV/Hu proteins can interfere with sexual differentiation. An ancient relationship to Sex-lethal is revealed by gonadal expression of RBP9, providing a maternal fail-safe for dosage compensation. Our results indicate that highly related ELAV/Hu RNA binding proteins select targets for mRNA processing through alteration of their expression levels and subcellular localization but only minimally by altered RNA binding specificity.
Securing Cluster-Based Ad Hoc Networks with Distributed Authorities

In this paper, we address key management in cluster-based mobile ad hoc networks (MANETs). Ensuring secure communication in an ad hoc network is extremely challenging because of the dynamic nature of the network and the lack of centralized management. For this reason, key management is particularly difficult to implement in such networks. We present a fully-distributed ID-based multiple secrets key management scheme (IMKM). This scheme is implemented via a combination of ID-based multiple secrets and threshold cryptography. It eliminates the need for certificate-based authenticated public-key distribution and provides an efficient mechanism for key update and key revocation schemes, which leads to more suitable, economic, adaptable, scalable, and autonomous key management for mobile ad hoc networks.
Trellis Coded Line Packing: Large Dimensional Beamforming Vector Quantization and Feedback Transmission

In this paper we study the beamforming vector quantization and feedback transmission problem for a cooperative transmission environment. Feedback is the primary means of providing the transmitter with channel state information (CSI) in a frequency division duplex (FDD) system. The conventional codebook approach uses a common codebook at the transmitter and at the receiver, while the feedback takes the form of the index of the codebook. This approach has a complexity that scales exponentially with the number of transmit antennas M, making the approach less favorable when M is large. We propose to use trellis-based quantization to reduce the complexity to grow linearly in M. A codebook design criteria is derived for the trellis-based quantizer. We also present three enhancements to the base scheme, each giving 0.2-0.8 dB gain. These enhancements address issues relevant to feedback error, trellis termination, and unequal path-loss from different transmission points. Performance results are shown in numerical simulations.
Linear Precoding for MIMO Multiple Access Channels with Finite Discrete Inputs

In this paper, we study linear precoding for multiple-input multiple-output (MIMO) multiple access channels (MAC) with finite discrete inputs. We derive the constellation-constrained capacity region for the MIMO MAC with an arbitrary number of users and find that the boundary can be achieved by solving the problem of weighted sum rate maximization with constellation and individual power constraints. Due to the non-concavity of the objective function, we obtain a set of necessary conditions for the optimization problem through Karush-Kuhn-Tucker analysis. To find the optimal precoding matrices for all users, we propose an iterative algorithm utilizing alternating optimization strategy. In particular, each iteration of the algorithm involves the gradient descent update with backtracking line search. Numerical results show that when inputs are digital modulated signals and the signal-to-noise ratio is in the medium range, our proposed algorithm offers considerably higher sum rate than non-precoding and the traditional method which maximizes Gaussian-input sum capacity. Furthermore, a low-density parity-check coded system with iterative detection and decoding for MAC is presented to evaluate the bit error rate (BER) performance of precoders. BER results also indicate that the system with the proposed linear precoder achieves significant gains over the non-precoding system and the precoder designed for Gaussian inputs.
A Key Regulator of Cell Adhesion: Identification and Characterization of Important N-Glycosylation Sites on Integrin α5 for Cell Migration

ABSTRACT The N-glycosylation of integrin α5β1 is thought to control many fundamental aspects of cell behavior, including cell adhesion and migration. However, the mechanism of how N-glycans function remains largely obscure. Here, we used a loss-of-function approach. Wild-type (WT) integrin α5 and N-glycosylation mutant S3-5 (sites 3 to 5) integrin α5, which contains fewer N-glycans, were stably reconstituted in α5 knockout cancer cells. We found that the migration ability of S3-5 cells was decreased in comparison with that of the WT. Interestingly, the levels of phosphorylated focal adhesion kinase and actin stress fiber formation were greatly enhanced in the S3-5 mutant. In a mechanistic manner, the internalization of active but not total integrin α5β1 was inhibited in S3-5 cells, which is a process that is related to the enhanced expression of active integrin α5β1 on the cell surface. Importantly, restoration of N-glycosylation on the β-propeller domain of α5 reinstated the cell migration ability, active α5β1 expression, and internalization. Moreover, these N-glycans are critical for α5–syndecan-4 complex formation. These findings indicate that N-glycosylation on the β-propeller domain functions as a molecular switch to control the dynamics of α5β1 on the cell surface that in turn is required for optimum adhesion for cell migration.
Characterization of Puma-Dependent and Puma-Independent Neuronal Cell Death Pathways following Prolonged Proteasomal Inhibition

ABSTRACT Proteasomal stress and the accumulation of polyubiquitinated proteins are key features of numerous neurodegenerative disorders. Previously we demonstrated that stabilization of p53 and activation of its target gene, puma (p53-upregulated mediator of apoptosis), mediated proteasome inhibitor-induced apoptosis in cancer cells. Here we demonstrated that Puma also contributed to proteasome inhibitor-induced apoptosis in mouse neocortical neurons. Although protection afforded by puma gene deletion was incomplete, we found little evidence indicating contributions from other proapoptotic BH3-only proteins. Attenuation of bax expression did not further reduce Puma-independent apoptosis, suggesting that pathways other than the mitochondrial apoptosis pathway were activated. Real-time imaging experiments in wild-type and puma-deficient neurons using a fluorescence resonance energy transfer (FRET)-based caspase sensor confirmed the involvement of a second cell death pathway characterized by caspase activation prior to mitochondrial permeabilization and, more prominently, a third, caspase-independent and Puma-independent pathway characterized by rapid cell shrinkage and nuclear condensation. This pathway involved lysosomal permeabilization in the absence of autophagy activation and was sensitive to cathepsin but not autophagy inhibition. Our data demonstrate that proteasomal stress activates distinct cell death pathways in neurons, leading to both caspase-dependent and caspase-independent apoptosis, and demonstrate independent roles for Puma and lysosomal permeabilization in this model.
Lack of seasonal variation in the incidence of eosinophilic oesophagitis in adolescent and adult non-PPI-responsive oesophageal eosinophilia midwestern US populations

Background Eosinophilic oesophagitis (EoO) has been associated with allergic disorders as well as aeroallergens. The current literature has shown a possible association between seasonal variation, mainly in the spring, and the incidence of EoO. However, this data was based on small population studies that did not exclude proton-pump inhibitor (PPI)-responsive oesophageal eosinophilia (PPI-ROE) in their cohort. Aim The aim of this study was to determine if there is a seasonal variation associated with the diagnosis of EoO in patients that had been treated with high-dose PPI prior to diagnosis. Methods Oesophageal biopsies were obtained from a cohort of patients who presented with symptoms of dysphagia, odynophagia, and heartburn during a 10-year period. Symptomatic patients who had biopsies from the mid and distal oesophagus with ≥20 eosinophils per high-power field (hpf) while on high-dose PPI treatment for at least 5 weeks were diagnosed as having EoO. The monthly and seasonal incidences were determined (winter, January–March; spring, April–June; summer, July–September; Autumn, October–December). Results A total of 20,718 patients were identified and their records evaluated. From this cohort, 193 (0.93%) symptomatic patients had biopsy-proven oesophageal eosinophilia (≥20 eosinophils/hpf) and no seasonal variation was seen in this group. However, only 57 (0.28%) had been adequately treated with PPI prior to diagnosis (i.e. non-PPI-ROE biopsy-proven EoO; ≥20 eosinophils/hpf: 39 males, 18 females; age 29.5 years). The most common medical history components included asthma (12.3%) and food allergies (3.5%), and the most common presenting symptoms included dysphagia (50.9%) and heartburn (26.3%). The monthly and seasonal incidences in our cohort were with no apparent trend (p = 0.713 and 0.703, respectively). Conclusions The incidence of EoO was consistent across all 12 months as well as during the four seasons. Our data does not support a seasonal variation in relation to the incidence of EoO in the US midwestern non-PPI-ROE population.
Life threatening spinal shock and complete neurological recovery following minor spinal cord trauma in a patient with pre-existing cervical canal stenosis: Case report

Mild to moderate trauma to the spinal cord that is complicated by existing cervical canal stenosis or spondylosis can be a life threatening event. It is against this background that we present a 41 year old male with cervical spinal stenosis who developed marked quadriparesis and respiratory embarrassment following collision with a colleague. He was admitted to the intensive care unit, electively sedated, paralysed and ventilated for a period of 48 hours. During the initial 24 hours of admission, he received methylprednisolone as per the National Acute Spinal Cord Injury Studies (NASCIS) protocol. Forty five hours later he had regained full neurological and respiratory function, allowing extubation and subsequent discharge from the intensive care unit. While patients with cervical spinal cord trauma in a setting of cervical canal stenosis or spondylosis can deteriorate dramatically, early recognition of this condition and prompt management using methylprednisolone, cervical stabilisation and ventilatory support during the initial window of opportunity will enable them make a full recovery.
On-Line Construction of Irregular Repeat Accumulate Codes for Packet Erasure Channels

In many applications erasure correcting codes are used to recover packet losses at high protocol stack layers. The objects (e.g. files) to be transmitted often have variable sizes, resulting in a variable number of packets to be encoded by the packet-level encoder. In this paper, algorithms for the (on-line) flexible design of parity-check matrices for irregular-repeat-accumulate codes are investigated. The proposed algorithms allow designing in fast manner parity-check matrices that are suitable for low-complexity maximum-likelihood decoding. The code ensembles generated by the algorithms are analyzed via extrinsic information transfer charts. Numerical results show how the designed codes can attain codeword error rates as low as 10-5 without appreciable losses w.r. t. the performance of idealized maximum-distance separable codes. Finally, we apply the proposed codes to the upcoming aeronautical communication standard, showing large performance improvements and proving the efficiency and the flexibility of the developed method.
Practice profile among endodontists in India: A nationwide questionnaire survey

Aim: The aim of this study was to ascertain endodontist's point of view (treatment philosophy, rationale and preference) regarding single and multiple-visit root canal treatment along with the basis on which the choice of treatment is made. Materials and Methods: The study was conducted on 500 endodontists of India through a comprehensive questionnaire asking about method of root-canal preparation, instrumentation, choice of irrigants and disinfectants among the participants. Results: A total of 444 filled survey forms out of 500 were finally evaluated in the study. Only 34% of endodontists always use rubber dam during root canal treatment, most of the endodontists preferred to do multiple visit root canal treatment and single visit root canal treatment was preferred mostly in vital tooth. 93% of the endodontists preferred to dress the canal between the visits. Conclusion: Within the limitations of this study it was concluded that most of the endodontists in India are still performing a root canal treatment in multiple visits and without using a rubber dam so the professional bodies in endodontics should embark on training programs, seminars and workshops aimed at improving the knowledge and skills of the endodontists.
Budd-Chiari syndrome

Budd-Chiari syndrome (BCS) is a rare and potentially life-threatening disorder characterized by obstruction of the hepatic outflow tract at any level between the junction of the inferior vena cava with the right atrium and the small hepatic veins. In the West, BCS is a rare hepatic manifestation of one or more underlying prothrombotic risk factors. The most common underlying prothrombotic risk factor is a myeloproliferative disorder, although it is now recognized that almost half of patients have multiple underlying prothrombotic risk factors. Clinical manifestations can be diverse, making BCS a possible differential diagnosis of many acute and chronic liver diseases. The index of suspicion should be very low if there is a known underlying prothrombotic risk factor and new onset of liver disease. Doppler ultrasound is sufficient for confirming the diagnosis, although tomographic imaging (computed tomography (CT) or magnetic resonance imaging (MRI)) is often necessary for further treatment and discussion with a multidisciplinary team. Anticoagulation is the cornerstone of the treatment. Despite the use of anticoagulation, the majority of patients need additional (more invasive) treatment strategies. Algorithms consisting of local angioplasty, TIPS and liver transplantation have been proposed, with treatment choice dictated by a lack of response to a less-invasive treatment regimen. The application of these treatment strategies allows for a five-year survival rate of 90%. In the long term the disease course of BCS can sometimes be complicated by recurrence, progression of the underlying myeloproliferative disorder, or development of post-transplant lymphoma in transplant patients.
The Imprinted Phlda2 Gene Regulates Extraembryonic Energy Stores

ABSTRACT An important difference between placental mammals and marsupials is the maturity of the fetus at birth. Placental mammals achieved this maturity by developing a complex and invasive placenta to support and prolong internal development. The exact genomic modifications that facilitated the evolution of this complex structure are unknown, but the emergence of genomic imprinting within mammalian lineages suggests a role for gene dosage. Here we show that a maximally altered placental structure is achieved by a single extra dose of the imprinted Phlda2 gene characterized by a dramatically reduced junctional zone and a decrease in stored glycogen. In addition, glycogen cells do not migrate into the maternal decidua in a timely fashion, but instead, Tpbpa-positive cells progressively mislocalize into the labyrinth. These defects are linked to a progressive restriction of embryonic growth from embryonic day 16.5. This work has identified a critical role for the imprinted Phlda2 gene in regulating glycogen storage in the eutherian placenta and implies that imprinting has provided a mechanism to boost nutrient supply to the fetus late in gestation, when the fetus is placing the highest demands on maternal resources, to enhance growth.
Sparsity-Inducing Direction Finding for Narrowband and Wideband Signals Based on Array Covariance Vectors

Among the existing sparsity-inducing direction-of-arrival (DOA) estimation methods, the sparse Bayesian learning (SBL) based ones have been demonstrated to achieve enhanced precision. However, the learning process of those methods converges much slowly when the signal-to-noise ratio (SNR) is relatively low. In this paper, we first show that the covariance vectors (columns of the covariance matrix) of the array output of independent signals share identical sparsity profiles corresponding to the spatial signal distribution, and their SNR exceeds that of the raw array output when moderately many snapshots are collected. Thus the SBL technique can be used to estimate the directions of independent narrowband/wideband signals by reconstructing those vectors with high computational efficiency. The method is then extended to narrowband correlated signals after proper modifications. In-depth analyses are also provided to show the lower bound of the new method in DOA estimation precision and the maximal signal number it can separate in the case of independent signals. Simulation results finally demonstrate the performance of the proposed method in both DOA estimation precision and computational efficiency.
A Multiple Aminoacyl-tRNA Synthetase Complex That Enhances tRNA-Aminoacylation in African Trypanosomes

ABSTRACT The genes for all cytoplasmic and potentially all mitochondrial aminoacyl-tRNA synthetases (aaRSs) were identified, and all those tested by RNA interference were found to be essential for the growth of Trypanosoma brucei. Some of these enzymes were localized to the cytoplasm or mitochondrion, but most were dually localized to both cellular compartments. Cytoplasmic T. brucei aaRSs were organized in a multiprotein complex in both bloodstream and procyclic forms. The multiple aminoacyl-tRNA synthetase (MARS) complex contained at least six aaRS enzymes and three additional non-aaRS proteins. Steady-state kinetic studies showed that association in the MARS complex enhances tRNA-aminoacylation efficiency, which is in part dependent on a MARS complex-associated protein (MCP), named MCP2, that binds tRNAs and increases their aminoacylation by the complex. Conditional repression of MCP2 in T. brucei bloodstream forms resulted in reduced parasite growth and infectivity in mice. Thus, association in a MARS complex enhances tRNA-aminoacylation and contributes to parasite fitness. The MARS complex may be part of a cellular regulatory system and a target for drug development.
Prognostic factors of hepatocellular carcinoma survival after radiofrequency ablation: A US population-based study

Objective To determine the survival outcome and prognostic factors of hepatocellular carcinoma (HCC) survival in patients who underwent radiofrequency ablation (RFA). Methods The Surveillance, Epidemiology and End Results (SEER) database was queried: There were 2588 HCC patients from 2004 to 2012 who underwent RFA. The Kaplan-Meier curves and the multivariate Cox regression analysis were used to assess the prognostic factors. Results With a median follow-up of 20 months, the 1-, 3- and 5-year overall survival (OS) rates were: 83%, 51% and 33%. Patients with a tumor size ≤5 cm in diameter had a better 5-year OS, as compared to patients with a tumor size >5 cm. The 5-year OS was significantly higher among patients with a normal level of alpha-fetoprotein (AFP), compared with those having elevated AFP. In an adjusted multivariate Cox regression analysis, those with ≥60 years of age (HR: 1.19; 95% CI 1.05–1.36), non-Asian race (HR: 1.53; 95% CI 1.30–1.81), tumor size >5 cm (HR: 1.43; 95% CI 1.24–1.65), elevated AFP (HR: 1.42; 95% CI 1.22–1.64), American Joint Committee on Cancer (AJCC) stages II-III (HR: 1.30; 95% CI 1.14–1.48) and the year of diagnosis from 2004–2007 (HR: 1.22; 95% CI 1.07–1.40) were significantly associated with a poor prognosis. Conclusions Age, race, tumor size, AFP level, AJCC stage and year of diagnosis were prognostic factors for OS in HCC patients who underwent RFA.
Otoacoustic emissions in noise-induced cochlear damage in artillery soldiers

Aim: Study the utility of distortion product otoacoustic emissions (DPOAEs) in the detection of preclinical noise-induced hearing loss (HL) in artillery soldiers. Materials and Methods: This cross-sectional study included all male subjects aged 18-35 years from the Indian Army and general civilians. Subjects underwent pure tone audiometry and DPOAE test. DPOAE parameters of subjects with normal hearing, nonexposed (control group 1 [CG1]) and noise exposed, HL (control group 2 [CG2]) were compared with noise exposed normal hearing (study group [SG]). Results: Mean DPOAE amplitude and sound to noise ratio of SG at all frequencies were significantly more than CG2 and less than CG1. SG had lower proportion of ears with absent DPOAEs than CG2, but higher than CG1 at all frequencies. Conclusions: Hearing loss is common among artillery soldiers. Artillery soldiers with normal hearing are more likely to develop HL due to impaired DPOAEs as compared to civilians with no history of noise exposure. Adequate safeguards are necessary to prevent handicap.