Miracle-dz/UniFAR-FTUs huggingface dataset:
The Transcriptome of the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus in Trichoplusia ni Cells

ABSTRACT Baculoviruses are important insect pathogens that have been developed as protein expression vectors in insect cells and as transduction vectors for mammalian cells. They have large double-stranded DNA genomes containing approximately 156 tightly spaced genes, and they present significant challenges for transcriptome analysis. In this study, we report the first comprehensive analysis of AcMNPV transcription over the course of infection in Trichoplusia ni cells, by a combination of strand-specific RNA sequencing (RNA-Seq) and deep sequencing of 5′ capped transcription start sites and 3′ polyadenylation sites. We identified four clusters of genes associated with distinctive patterns of mRNA accumulation through the AcMNPV infection cycle. A total of 218 transcription start sites (TSS) and 120 polyadenylation sites (PAS) were mapped. Only 29 TSS were associated with a canonical TATA box, and 14 initiated within or near the previously identified CAGT initiator motif. The majority of viral transcripts (126) initiated within the baculovirus late promoter motif (TAAG), and late transcripts initiated precisely at the second position of the motif. Analysis of 3′ ends showed that 92 (77%) of the 3′ PAS were located within 30 nucleotides (nt) downstream of a consensus termination signal (AAUAAA or AUUAAA). A conserved U-rich region was found approximately 2 to 10 nt downstream of the PAS for 58 transcripts. Twelve splicing events and an unexpectedly large number of antisense RNAs were identified, revealing new details of possible regulatory mechanisms controlling AcMNPV gene expression. Combined, these data provide an emerging global picture of the organization and regulation of AcMNPV transcription through the infection cycle.
Habituation of horses to treadmill locomotion

Summary Habituation to treadmill locomotion was investigated in ten Dutch Warmblood horses during a one-week training programme. Kinematics of the horses were recorded using a CODA-3 system and unidirectional accelerometers attached to all hooves. Horses were exercised for five days, twice a day at the walk and trot for five minutes at both gaits. Temporal and spatial stride variables and vertical trunk movement were analysed. The results indicate differences in habituation between different variables and gaits. At the walk, changes in stride duration and limb movement angle were found up to the last measurement. At the trot, all variables including constancy of stride approached constant values by the third session. At the beginning of each training session rapid adaptation occurred, disregarding the first minute of a session for locomotion studies. In conclusion, locomotion analysis at the trot requires training for a minimum of two sessions. For measurements at the walk, longer periods are recommended.
Pain Coping Strategies Following Traumatic Brain Injury

Objective:To investigate the pain coping strategies and adjustment levels of chronic pain patients who had sustained a traumatic brain injury (TBI). Design:A case-control study that matched TDI and non-TBI chronic pain patients who had a history of at least 6 months of pain. Setting:TBI patients were recruited from an adult tertiary care center brain injury clinic, and non-TBI patients were recruited from an adult tertiary care center pain clinic. Patients:The study evaluated a consecutive sample of 36 TBI patients and 36 non-TBI patients. TBI and non-TBI patients were matched for gender, type of pain, pain severity, and pain frequency. Main Outcome Measures:Patients completed the Coping Strategy Questionnaire, the Multidimensional Pain Inventory, the Pain Disability Index, and the Beck Depression Inventory. Results:Although patients who had sustained a TBI reported less control over their pain, they also reported less suffering and less interference in daily activities than patients who had not sustained a TBI. Conclusions:Patients who have sustained a TBI may utilize pain monitoring and pain coping skills differently from non- TBI pain patients. Development of pain measures and pain management strategies that account for TBI patients' specific needs may be appropriate.
The Viral Gene ORF79 Encodes a Repressor Regulating Induction of the Lytic Life Cycle in the Haloalkaliphilic Virus ϕCh1

ABSTRACT In this study, we describe the construction of the first genetically modified mutant of a halovirus infecting haloalkaliphilic Archaea. By random choice, we targeted ORF79, a currently uncharacterized viral gene of the haloalkaliphilic virus ϕCh1. We used a polyethylene glycol (PEG)-mediated transformation method to deliver a disruption cassette into a lysogenic strain of the haloalkaliphilic archaeon Natrialba magadii bearing ϕCh1 as a provirus. This approach yielded mutant virus particles carrying a disrupted version of ORF79. Disruption of ORF79 did not influence morphology of the mature virions. The mutant virus was able to infect cured strains of N. magadii, resulting in a lysogenic, ORF79-disrupted strain. Analysis of this strain carrying the mutant virus revealed a repressor function of ORF79. In the absence of gp79, onset of lysis and expression of viral proteins occurred prematurely compared to their timing in the wild-type strain. Constitutive expression of ORF79 in a cured strain of N. magadii reduced the plating efficiency of ϕCh1 by seven orders of magnitude. Overexpression of ORF79 in a lysogenic strain of N. magadii resulted in an inhibition of lysis and total absence of viral proteins as well as viral progeny. In further experiments, gp79 directly regulated the expression of the tail fiber protein ORF34 but did not influence the methyltransferase gene ORF94. Further, we describe the establishment of an inducible promoter for in vivo studies in N. magadii. IMPORTANCE Genetic analyses of haloalkaliphilic Archaea or haloviruses are only rarely reported. Therefore, only little insight into the in vivo roles of proteins and their functions has been gained so far. We used a reverse genetics approach to identify the function of a yet undescribed gene of ϕCh1. We provide evidence that gp79, a currently unknown protein of ϕCh1, acts as a repressor protein of the viral life cycle, affecting the transition from the lysogenic to the lytic state of the virus. Thus, repressor genes in other haloviruses could be identified by sequence homologies to gp79 in the future. Moreover, we describe the use of an inducible promoter of N. magadii. Our work provides valuable tools for the identification of other unknown viral genes by our approach as well as for functional studies of proteins by inducible expression.
Intracellular Transport of Vaccinia Virus in HeLa Cells Requires WASH-VPEF/FAM21-Retromer Complexes and Recycling Molecules Rab11 and Rab22

ABSTRACT Vaccinia virus, the prototype of the Orthopoxvirus genus in the family Poxviridae, infects a wide range of cell lines and animals. Vaccinia mature virus particles of the WR strain reportedly enter HeLa cells through fluid-phase endocytosis. However, the intracellular trafficking process of the vaccinia mature virus between cellular uptake and membrane fusion remains unknown. We used live imaging of single virus particles with a combination of various cellular vesicle markers, to track fluorescent vaccinia mature virus particle movement in cells. Furthermore, we performed functional interference assays to perturb distinct vesicle trafficking processes in order to delineate the specific route undertaken by vaccinia mature virus prior to membrane fusion and virus core uncoating in cells. Our results showed that vaccinia virus traffics to early endosomes, where recycling endosome markers Rab11 and Rab22 are recruited to participate in subsequent virus trafficking prior to virus core uncoating in the cytoplasm. Furthermore, we identified WASH-VPEF/FAM21-retromer complexes that mediate endosome fission and sorting of virus-containing vesicles prior to virus core uncoating in the cytoplasm. IMPORTANCE Vaccinia mature virions of the WR strain enter HeLa cells through fluid phase endocytosis. We previously demonstrated that virus-containing vesicles are internalized into phosphatidylinositol 3-phosphate positive macropinosomes, which are then fused with Rab5-positive early endosomes. However, the subsequent process of sorting the virion-containing vesicles prior to membrane fusion remains unclear. We dissected the intracellular trafficking pathway of vaccinia mature virions in cells up to virus core uncoating in cytoplasm. We show that vaccinia mature virions first travel to early endosomes. Subsequent trafficking events require the important endosome-tethered protein VPEF/FAM21, which recruits WASH and retromer protein complexes to the endosome. There, the complex executes endosomal membrane fission and cargo sorting to the Rab11-positive and Rab22-positive recycling pathway, resulting in membrane fusion and virus core uncoating in the cytoplasm.
High-speed and low-power multipliers using the Baugh-Wooley algorithm and HPM reduction tree

The modified-Booth algorithm is extensively used for high-speed multiplier circuits. Once, when array multipliers were used, the reduced number of generated partial products significantly improved multiplier performance. In designs based on reduction trees with logarithmic logic depth, however, the reduced number of partial products has a limited impact on overall performance. The Baugh-Wooley algorithm is a different scheme for signed multiplication, but is not so widely adopted because it may be complicated to deploy on irregular reduction trees. We use the Baugh-Wooley algorithm in our High Performance Multiplier (HPM) tree, which combines a regular layout with a logarithmic logic depth. We show for a range of operator bit-widths that, when implemented in 130-nm and 65-nm process technologies, the Baugh-Wooley multipliers exhibit comparable delay, less power dissipation and smaller area foot-print than modified-Booth multipliers.
Ovarian cancer in older women

Age-specific analysis reveals that the incidence of and mortality rate from ovarian cancer are continuously increasing in the elderly population. The incidence of ovarian cancer rises steadily with advancing age during adulthood and peaks in the seventh and eighth decades of life. The prognosis of elderly ovarian cancer patients is worse than that of their younger counterparts. It is the opinion of the authors that the majority of clinicians seem to be unprepared to treat elderly patients, and many data indicate that a great number of patients are undertreated due to the fear of unacceptable side effects, thus limiting their possibility of survival. Guidelines are clearly needed, including advice on whether to treat at all and whether standard surgery or chemotherapy are feasible in elderly patients with ovarian cancer. In this report, four basic aspects of ovarian cancer in the elderly will be focused on: the most important factors affecting prognosis, the safety of surgical treatment in older patients, .
An over-voltage protection circuit for CMOS power amplifiers

With increasing demand for higher integration and lower cost of mobile communication devices there is a growing trend towards the use of CMOS power amplifiers (PAs) instead of GaAs or SiGe PAs. Although being comparatively inexpensive, CMOS not only suffers from inferior RF performance but also from low breakdown voltages. This gets an issue especially for the PA output stage, when load mismatches lead to high voltage-standing wave ratios (VSWR) and therefore high peak voltages at the PA output. In this work a 27 dBm PA in 0.13 mum CMOS with an integrated VSWR protection circuit is presented. A control loop detects critically high voltage amplitudes at the PA output and reduces the PA gain in order to lower the output voltage swing to uncritical values.
Research for the Inclusion of Home-Based Physical Therapy in Long-Term Care Insurance System of Physical Therapists in Elderly Care Facilities

This study of the elderly in the future expansion of long-term care insurance as a priority landing at the introduction of physical therapy services aim to provide baseline data and long-term care insurance for him, the elderly that provides physical therapy services under the elderly property of a physical therapist recognition system for the investigation was conducted. As a result, the perception of the elderly long-term care insurance was higher by 88.1% of the higher needs, but also the absolute need for more than 40 years of age the response was higher with 60.3 percent. In addition, the number of visits that care should be priced higher relative to the 59.7 percent was the highest opinion. Visit of physical therapy services include the most important therapeutic approach to life and 40% was the highest forum, visit the Nursing Center as a service principal points that you need to visit the rehab center, accounting for 69.4 percent opinion. The expected effect of physical therapy visits conducted in a 50-point scale showed an overall average 41.44 points and 42.48 points, especially over the age of 40 appear in the overall expected effect was higher.
Triple modality testing by endoscopic retrograde cholangiopancreatography for the diagnosis of cholangiocarcinoma

Objectives: Brush cytology has a low sensitivity for the diagnosis of cholangiocarcinoma. This study aimed to compare the standard approach (brush cytology) with a triple modality approach utilizing brush cytology, forceps biopsy and fluorescence in situ hybridization in terms of sensitivity and specificity for the diagnosis of cholangiocarcinoma. Methods: In a retrospective study at a single academic center, 50 patients underwent triple modality testing. Additionally, 61 patients underwent brush cytology alone. Intervention was endoscopic retrograde cholangiopancreatography with brush cytology, fluorescence in situ hybridization, and forceps biopsy. The main outcome measures included sensitivity, specificity, positive predictive value and negative predictive value. Results: Overall, 50 patients underwent triple tissue sampling, and 61 patients underwent brush cytology alone. Twenty-two patients were eventually diagnosed with cholangiocarcinoma. Brush cytology had a sensitivity of 42%, specificity of 100%, positive predictive value of 100% and negative predictive value of 88%. Triple tissue sampling had an overall sensitivity of 82%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 87%. Within the triple test group, brush cytology had a sensitivity of 27%, forceps biopsy had a sensitivity of 50%, and fluorescence in situ hybridization analysis had a sensitivity of 59%. Conclusions: A triple modality approach results in a marked increase in sensitivity for the diagnosis of cholangiocarcinoma compared with single modality testing such as brush cytology and should be considered in the evaluation of indeterminate or suspicious biliary strictures.
Protein Kinase PKR-Dependent Activation of Mitogen-Activated Protein Kinases Occurs through Mitochondrial Adapter IPS-1 and Is Antagonized by Vaccinia Virus E3L

ABSTRACT The p38 and c-Jun N-terminal kinase (JNK) mitogen-activated protein kinases (MAPKs) play important roles in the host innate immune response. The protein kinase regulated by RNA (PKR) is implicated in p38 MAPK activation in response to proinflammatory signals in mouse embryonic fibroblasts. To test the role of PKR in the activation of p38 and JNK MAPKs in human cells following viral infection, HeLa cells made stably deficient in PKR by using an RNA interference strategy were compared to cells with sufficient PKR. The phosphorylation of both p38 and JNK in cells with sufficient PKR was activated following either infection with an E3L deletion (ΔE3L) mutant of vaccinia virus or transfection with double-stranded RNA (dsRNA) in the absence of infection with wild-type vaccinia virus. The depletion of PKR by stable knockdown impaired the phosphorylation of both p38 and JNK induced by either the ΔE3L mutant virus or dsRNA but not that induced by tumor necrosis factor alpha. The PKR-dependent activation of MAPKs in ΔE3L mutant-infected cells was abolished by treatment with cytosine β-d-arabinoside. The complementation of PKR-deficient cells with the human PKR wild-type protein, but not with the PKR catalytic mutant (K296R) protein, restored p38 and JNK phosphorylation following ΔE3L mutant virus infection. Transient small interfering RNA knockdown established that the p38 and JNK kinase activation following ΔE3L infection was dependent upon RIG-I-like receptor signal transduction pathway components, including the mitochondrial adapter IPS-1 protein.
Mutagenesis of the DI/DIII Linker in Dengue Virus Envelope Protein Impairs Viral Particle Assembly

ABSTRACT The dengue virus (DV) envelope (E) protein is important in mediating viral entry and assembly of progeny virus during cellular infection. Domains I and III (DI and DIII, respectively) of the DV E protein are connected by a highly conserved but poorly ordered region, the DI/DIII linker. Although the flexibility of the DI/DIII linker is thought to be important for accommodating the structural rearrangements undergone by the E protein during viral entry, the function of the linker in the DV infectious cycle is not well understood. In this study, we performed site-directed mutagenesis on conserved residues in the DI/DIII linker of the DV2 E protein and showed that the resulting mutations had little or no effect on the entry process but greatly affected virus assembly. Biochemical fractionation and immunofluorescence microscopy experiments performed on infectious virus as well as in a virus-like particle (VLP) system indicate that the DI/DIII linker mutants express the DV structural proteins at the sites of particle assembly near the ER but fail to form infectious particles. This defect is not due to disruption of E's interaction with prM and pr in immature and mature virions, respectively. Serial passaging of the DV2 mutant E-Y299F led to the identification of a mutation in the membrane-proximal stem region of E that fully compensates for the assembly defect of this DI/DIII linker mutant. Together, our results suggest a critical and previously unidentified role for the E protein DI/DIII linker region during the DV2 assembly process.
Cullin4A and Cullin4B Are Interchangeable for HIV Vpr and Vpx Action through the CRL4 Ubiquitin Ligase Complex

ABSTRACT Human immunodeficiency virus (HIV) seizes control of cellular cullin-RING E3 ubiquitin ligases (CRLs) to promote viral replication. HIV-1 Vpr and HIV-2/simian immunodeficiency virus (SIV) Vpr and Vpx engage the cullin4 (CUL4)-containing ubiquitin ligase complex (CRL4) to cause polyubiquitination and proteasomal degradation of host proteins, including ones that block infection. HIV-1 Vpr engages CRL4 to trigger the degradation of uracil-N-glycosylase 2 (UNG2). Both HIV-1 Vpr and HIV-2/SIV Vpr tap CRL4 to initiate G2 cell cycle arrest. HIV-2/SIV Vpx secures CRL4 to degrade the antiviral protein SAMHD1. CRL4 includes either cullin4A (CUL4A) or cullin4B (CUL4B) among its components. Whether Vpr or Vpx relies on CUL4A, CUL4B, or both to act through CRL4 is not known. Reported structural, phenotypic, and intracellular distribution differences between the two CUL4 types led us to hypothesize that Vpr and Vpx employ these in a function-specific manner. Here we determined CUL4 requirements for HIV-1 and HIV-2/SIV Vpr-mediated G2 cell cycle arrest, HIV-1 Vpr-mediated UNG2 degradation, and HIV-2 Vpx-mediated SAMHD1 degradation. Surprisingly, CUL4A and CUL4B are exchangeable for CRL4-dependent Vpr and Vpx action, except in primary macrophages, where Vpx relies on both CUL4A and CUL4B for maximal SAMHD1 depletion. This work highlights the need to consider both CUL4 types for Vpr and Vpx functions and also shows that the intracellular distribution of CUL4A and CUL4B can vary by cell type. IMPORTANCE The work presented here shows for the first time that HIV Vpr and Vpx do not rely exclusively on CUL4A to cause ubiquitination through the CRL4 ubiquitin ligase complex. Furthermore, our finding that intracellular CUL4 and SAMHD1 distributions can vary with cell type provides the basis for reconciling previous disparate findings regarding the site of SAMHD1 depletion. Finally, our observations with primary immune cells provide insight into the cell biology of CUL4A and CUL4B that will help differentiate the functions of these similar proteins.
New and emerging therapies for the treatment of irritable bowel syndrome: an update for gastroenterologists

Irritable bowel syndrome is a functional bowel disorder with gastrointestinal symptoms (e.g. abdominal pain, straining, urgency, incomplete evacuation, nausea, and bloating) that occur alongside bowel function alterations (i.e. constipation, diarrhea, or both). Patients with irritable bowel syndrome may also experience comorbid anxiety and depression. Irritable bowel syndrome is common, with a prevalence estimated between 3% and 28%, affecting patient health and quality of life. Patients with moderate or severe irritable bowel syndrome generally seek medical care, whereas those with milder symptoms may choose self-management. Most patients with irritable bowel syndrome receive outpatient care, but irritable bowel syndrome-related hospitalizations do occur. The pathophysiology of irritable bowel syndrome is multifactorial (i.e. genetics, immune components, changes in the gut microbiota, disturbances in physiologic stress response systems, and psychosocial factors). Management of irritable bowel syndrome can include lifestyle changes, dietary interventions, counseling, psychologic medication, and agents that affect gastrointestinal motility. A number of therapies have emerged in recent years with clinical trial data demonstrating efficacy and safety for patients with irritable bowel syndrome, including agents that target gastrointestinal motility (i.e. linaclotide), gastrointestinal opioid receptors (i.e. asimadoline, eluxadoline), and gut microbiota (i.e. rifaximin). Linaclotide has been shown to significantly improve stool frequency and abdominal pain compared with placebo in constipation-predominant irritable bowel syndrome (number needed to treat, 5.1). Asimadoline shows efficacy in patients with moderate-to-severe irritable bowel syndrome-related pain. Rifaximin provided adequate relief of global irritable bowel syndrome symptoms versus placebo for a significantly greater percentage of patients with diarrhea-predominant irritable bowel syndrome (p < 0.001). Management that encompasses all aspects of irritable bowel syndrome (gastrointestinal symptoms) and comorbid psychologic symptoms (e.g. anxiety or depression) is important for improving overall patient health and well-being.