Miracle-dz/UniFAR-FTUs huggingface dataset:
Herpesvirus saimiri MicroRNAs Preferentially Target Host Cell Cycle Regulators

ABSTRACT In latently infected marmoset T cells, Herpesvirus saimiri (HVS) expresses six microRNAs (known as miR-HSURs [H. saimiri U-rich RNAs]). The viral miR-HSURs are processed from chimeric primary transcripts, each containing a noncoding U-rich RNA (HSUR) and a pre-miRNA hairpin. To uncover the functions of miR-HSURs, we identified mRNA targets in infected cells using high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). HITS-CLIP revealed hundreds of robust Argonaute (Ago) binding sites mediated by miR-HSURs that map to the host genome but few in the HVS genome. Gene ontology analysis showed that several pathways regulating the cell cycle are enriched among cellular targets of miR-HSURs. Interestingly, miR-HSUR4-3p represses expression of the p300 transcriptional coactivator by binding the open reading frame of its mRNA. miR-HSUR5-3p directly regulates BiP, an endoplasmic reticulum (ER)-localized chaperone facilitating maturation of major histocompatibility complex class I (MHC-I) and the antiviral response. miR-HSUR5-3p also robustly downregulates WEE1, a key negative regulator of cell cycle progression, leading to reduced phosphorylation of its substrate, cyclin-dependent kinase (Cdk1). Consistently, inhibition of miR-HSUR5-3p in HVS-infected cells decreases their proliferation. Together, our results shed light on the roles of viral miRNAs in cellular transformation and viral latency. IMPORTANCE Viruses express miRNAs during various stages of infection, suggesting that viral miRNAs play critical roles in the viral life cycle. Compared to protein-coding genes, the functions of viral miRNAs are not well understood. This is because it has been challenging to identify their mRNA targets. Here, we focused on the functions of the recently discovered HVS miRNAs, called miR-HSURs. HVS is an oncogenic gammaherpesvirus that causes acute T-cell lymphomas and leukemias in New World primates and transforms human T cells. A better understanding of HVS biology will help advance our knowledge of virus-induced oncogenesis. Because numerous cellular miRNAs play crucial roles in cancer, viral miRNAs from the highly oncogenic HVS might also be important for transformation. Here, we found that the miR-HSURs preferentially modulate expression of host cell cycle regulators, as well as antiviral response factors. Our work provides further insight into the functions of herpesviral miRNAs in virus-induced oncogenesis and latency.
Implementation and performance evaluation of mmWave channel sounding system

This paper introduces mBECS(millimeter wave Band Exploration and Channel Sounder), also known as channel sounder, to explore mmWave channel characteristic. We present engineering parameters for implementation of the mmWave channel sounder to use swept time delay cross-correlation(STDCC) technique and show the measurement results of system response obtained from performance evaluation test. The dynamic range above 45 dB was obtained at 28GHz.
Transport properties of degenerate electrons in neutron star envelopes and white dwarf cores

New calculations of the thermal and electrical elec- tron conductivities are performed for a broad range of physi- cal parameters typical for envelopes of neutron stars and cores of white dwarfs. We consider stellar matter composed of as- trophysically important chemical elements from H to Fe in the density range from 10 2 -10 4 gc m 3 up to 10 7 -10 10 gc m 3 , where atoms are fully ionized and electrons are strongly degen- erate. We have used modified ion structure factors suggested recently by Baiko et al. (1998). In the ion liquid, these mod- ifications take into account, in an approximate way, instan- taneous electron-band structures that reduce the electron-ion scattering rate. In crystallized matter, the new structure factors include multi-phonon processes important at temperatures not very much lower than the melting temperature Tm. The trans- port coefficients obtained differ significantly from those derived earlier in the important temperature range Tm=5 < T < 5Tm.
The Floating-Point Extension of Symbolic Execution Engine for Bug Detection

Many existing symbolic execution engines for bug detection often ignore floating-point types and operations. That will result in imprecise reasoning about the feasibility of program paths, which in turn leads to false positives and negatives. Recently, there are quite some progress in satisfiability modulo theories (SMT) solving, and some tools are able to support floating-point arithmetic. Nevertheless, naturally extending a symbolic execution engine and directly replacing the back-end with the new SMT solver will not make a good static analyzer for floating-point programs.In this paper, we extend an existing symbolic execution engine for C program bug finding, so that it can deal with floating-point arithmetic and mathematical functions. For the mathematical functions, we employ an abstract model to keep a balance between overhead and precision. We also introduce a strategy, Lazy-verification, to reduce the number of SMT solver calls. We implemented our approach as a tool called Canalyze-fp. Experiments with self-developed benchmarks and non-trivial open source programs show that the proposed approach can effectively avoid the false positives and negatives, without introducing too much overhead.
The selective intermediate nodes scheme for ad hoc on-demand routing protocols

The on-demand routing schemes in mobile ad hoc networks are appealing because of the lower routing overhead, compared with traditional proactive schemes. The on-demand routing protocols introduce routing overhead only in the presence of data packets that need routes. However, the control overhead of on-demand routing schemes increases with node geographic density and traffic pattern density. In fact, this is an undesirable feature for the scalable routing protocols whose control overhead should be under control to keep up with increasing offered load. As a solution for such a drawback of current reactive routing schemes, we propose the selective intermediate nodes mechanism. In this protocol, each node adaptively propagates routing information based on the local load level and cluster status. The local load level (local load status), based on channel utilization and queue size, reflects the load of the node in question and of all of its neighbors; the cluster status denotes the role of a node in a cluster (i.e., a cluster head, gateway or ordinary node). We demonstrate the effectiveness of our enhancement by applying it to ad hoc on-demand distance vector routing (AODV) and dynamic source routing (DSR). Simulation results show that the proposed idea significantly reduces the control overhead and improves the overall performance and scalability of the routing protocols.
Perfiles de estudiantes mexicanos con aptitudes intelectuales sobresalientes

The study was aimed to determine whether achievement motivation and social self-concept allowed identifying clusters of intellectually outstanding high school students. A classification design with a quantitative methodology was applied whereby, by simple random sampling, 133 outstanding students were selected. Two clusters of students were identified: the first, known as 'Highly achievement oriented', and the second as 'Lowly achievement oriented', respectively. Students of the first cluster were characterized by a greater motivation toward academic achievement, lower social self-concept and higher academic average. It was concluded that in motivational and emotional aspects outstanding students show significant differences which suggests being careful with generalizations made without empirical support. The study also showed the importance of identifying individual differences as part of the counseling and tutoring strategies with these students.
SiZer for jump detection

SiZer is an exploratory graphical method for . nding structure in data. When the structure is a jump in the underlying curve, a “jump funnel” is created in the SiZer map. The shape of this funnel is analyzed. The result is the basis of a proposed variation of SiZer that is specially tuned to . nding jumps. Acknowledgement 1 Research of C. S. Kim was supported by a Cheju National University Research Grant, 1997.
Unconstrained speculative execution with predicated state buffering

Speculative execution is execution of instructions before it is known whether these instructions should be executed. Compiler-based speculative execution has the potential to achieve both a high instruction per cycle rate and high clock rate. Pure compiler-based approaches, however have greatly limited instruction scheduling due to a limited ability to handle side effects of speculative execution. Significant performance improvement is, thus, difficult in non-numerical applications. This paper proposes a new architectural mechanism, called predicating, which provides unconstrained speculative execution. Predicating removes restrictions which limit the compiler's ability to schedule instructions. Through our hardware support, the compiler is allowed to move instructions past multiple basic block boundaries from any succeeding control path. Predicating buffers the side effects of speculative execution with its predicate, and the buffered predicate efficiently commits or squashes the side effects. The mechanism also provides a speculative exception handling scheme. The scheme, called the future condition properly postpones speculative exceptions and efficiently restarts the process. We show that our mechanism can be implemented through a modest amount of hardware with little complexity. The evaluation results show that our mechanism significantly improves performane, and achieves a 2.45x speedup over scalar machines.
Nontypeable Haemophilus influenzae Strain 2019 Produces a Biofilm Containing N-Acetylneuraminic Acid That May Mimic Sialylated O-Linked Glycans

ABSTRACT Previous studies suggested that nontypeable Haemophilus influenzae (NTHI) can form biofilms during human and chinchilla middle ear infections. Microscopic analysis of a 5-day biofilm of NTHI strain 2019 grown in a continuous-flow chamber revealed that the biofilm had a diffuse matrix interlaced with multiple water channels. Our studies showed that biofilm production was significantly decreased when a chemically defined medium lacking N-acetylneuraminic acid (sialic acid) was used. Based on these observations, we examined mutations in seven NTHI strain 2019 genes involved in carbohydrate and lipooligosaccharide biosynthesis. NTHI strain 2019 with mutations in the genes encoding CMP-N-acetylneuraminic acid synthetase (siaB), one of the three NTHI sialyltransferases (siaA), and the undecaprenyl-phosphate α-N-acetylglucosaminyltransferase homolog (wecA) produced significantly smaller amounts of biofilm. NTHI strain 2019 with mutations in genes encoding phosphoglucomutase (pgm), UDP-galactose-4-epimerase, and two other NTHI sialyltransferases (lic3A and lsgB) produced biofilms that were equivalent to or larger than the biofilms produced by the parent strain. The biofilm formed by the NTHI strain 2019pgm mutant was studied with Maackia amurensis fluorescein isothiocyanate (FITC)-conjugated and Sambucus nigra tetramethyl rhodamine isocyanate (TRITC)-conjugated lectins. S. nigra TRITC-conjugated lectin bound to this biofilm, while M. amurensis FITC-conjugated lectin did not. S. nigra TRITC-conjugated lectin binding was inhibited by incubation with α2,6-neuraminyllactose and by pretreatment of the biofilm with Vibrio cholerae neuraminidase. Matrix-assisted laser desorption ionization—time of flight mass spectometry analysis of lipooligosaccharides isolated from a biofilm, the planktonic phase, and plate-grown organisms showed that the levels of most sialylated glycoforms were two- to fourfold greater when the lipooligosaccharide was derived from planktonic or biofilm organisms. Our data indicate that NTHI strain 2019 produces a biofilm containing α2,6-linked sialic acid and that the sialic acid content of the lipooligosaccharides increases concomitant with the transition of organisms to a biofilm form.
Evaluating Formulations of Stable Boundary Layer Height

Abstract Stable boundary layer height h is determined from eddy correlation measurements of the vertical profiles of the buoyancy flux and turbulence energy from a tower over grassland in autumn, a tower over rangeland with variable snow cover during winter, and aircraft data in the stable marine boundary layer generated by warm air advection over a cool ocean surface in summer. A well-defined h within the tower layer at the grass site (lowest 50 m) and the snow site (lowest 30 m) was definable only about 20% of the time. In the remaining stable periods, the buoyancy flux and turbulence energy either (a) remained constant with height, indicating a deep boundary layer, (b) increased with height, or (c) varied erratically with height. Approximately one-half of the tower profiles did not fit the traditional concepts of a boundary layer. The well-defined cases of h are compared with various formulations for the equilibrium depth of the stably stratified boundary layer based on the Richardson number or surface.
Reorientations, relaxations, metastabilities, and multidomains of skyrmion lattices

Magnetic skyrmions are nanosized topologically protected spin textures with particlelike properties. They can form lattices perpendicular to the magnetic field, and the orientation of these skyrmion lattices with respect to the crystallographic lattice is governed by spin-orbit coupling. By performing small-angle neutron scattering measurements, we investigate the coupling between the crystallographic and skyrmion lattices in both ${\mathrm{Cu}}_{2}{\mathrm{OSeO}}_{3}$ and the archetype chiral magnet MnSi. The results reveal that the orientation of the skyrmion lattice is primarily determined by the magnetic field direction with respect to the crystallographic lattice. In addition, it is also influenced by the magnetic history of the sample, which can induce metastable lattices. Kinetic measurements show that these metastable skyrmion lattices may or may not relax to their equilibrium positions under macroscopic relaxation times. Furthermore, multidomain lattices may form when two or more equivalent crystallographic directions are favored by spin-orbit coupling and oriented perpendicular to the magnetic field.
Use of Diagnosis Codes and/or Wound Culture Results for Surveillance of Surgical Site Infection after Mastectomy and Breast Reconstruction

We compared surveillance of surgical site infection (SSI) after major breast surgery by using a combination of International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis codes and microbiology-based surveillance. The sensitivity of the coding algorithm for identification of SSI was 87.5%, and the sensitivity of wound culture for identification of SSI was 78.1%. Our results suggest that SSI surveillance can be reliably performed using claims data.
Do continued antidepressants protect against dementia in patients with severe depressive disorder?

Studies on humans show that depressive disorder is associated with an increased risk of developing cognitive dysfunction, and animal studies suggest that antidepressants may have neuroprotective abilities. On the basis of these observations, it was hypothesized that treatment with antidepressants may decrease the risk of developing dementia in patients with depression. We investigated whether continued treatment with antidepressants is associated with a decreased rate of dementia in a population of patients discharged from psychiatric healthcare service with a diagnosis of depression. We used register data on all prescribed antidepressants in all patients discharged from psychiatric healthcare service with a diagnosis of depression and with subsequent diagnoses of dementia in Denmark from 1995 to 2005. A total of 37 658 patients with a diagnosis of depression at their first psychiatric contact and who were exposed to antidepressants after discharge were included in the study. A total of 2007 patients (5.3%) were subsequently diagnosed with dementia of any kind. The rate of dementia decreased during periods of two or more prescriptions of older antidepressants compared with the period of only one prescription of older antidepressants [relative risk (RR)=0.83 (95% confidence interval (CI)=0.70–0.98)]. This finding was replicated with Alzheimer’s disease as the outcome [RR=0.66 (95% CI=0.47–0.94)] but not with dementia of other kinds as the outcome [RR=0.88 (95% CI=0.73–1.06)]. In contrast, during periods of continued use of selective serotonin reuptake inhibitors or newer nonselective serotonin reuptake inhibitors, the rate of dementia was not decreased, regardless of the subtype of dementia. It was concluded that continued long-term treatment with older antidepressants is associated with a reduced rate of dementia in patients treated in psychiatric healthcare settings, whereas continued treatment with other kinds of antidepressants is not. Methodological reasons for these findings cannot be excluded because of the nonrandomized nature of data.
Detection and gram discrimination of bacterial pathogens from aqueous and vitreous humor using real-time PCR assays.

PURPOSE To develop and apply real-time PCR protocols to the detection and classification of the Gram status of bacterial pathogens in aqueous and vitreous humor collected from clinically suspected intraocular infections. METHODS The analytical specificity of two PCR assays, SYBR Green 16S rDNA-Based Universal PCR (SGRU-PCR), and a Multiplex Gram-Specific TaqMan-Based PCR (MGST-PCR), was determined with 31 clinically important pathogens, including 20 Gram-positive and 11 Gram-negative. Analytical sensitivity was determined with a 10-fold dilution of Staphylococcus epidermidis and Escherichia coli DNA. Assays were further tested on aqueous (n = 10) and vitreous humor (n = 11) samples collected from patients with clinically diagnosed intraocular infections. RESULTS DNA was amplified from all control bacterial isolates when using SGRU-PCR. MGST-PCR correctly classified the Gram status of all these isolates. The SGRU-PCR limit of detection of S. epidermidis and E. coli DNA was 100 fg/μL (E = 0.82 and 0.86; r(2) = 0.99) and for MGST-PCR, 1 pg/μL (E = 0.66 and 0.70; r(2) = 0.99. For clinical intraocular samples, positivity of culture was 47.6% and for real-time PCR assays, 95.2%. Gram classification was achieved in 100% of MGST-PCR-positive samples. Among microbiologically negative samples, real-time PCR assays were positive in 90% of cases. The false-positive rate in control aqueous was 3.2%, and control samples of vitreous were negative. CONCLUSIONS The real-time PCR assays demonstrated good correlation, with culture-proven RESULTS With the use of these methods, bacterial detection was improved from 47.6% to 95.3%, demonstrating them to be sensitive, rapid tests for diagnosis of bacterial endophthalmitis.
The Role of MAP Kinases in Trauma and Ischemia–Reperfusion

Mitogen-activated protein kinases (MAPKs) have been the focus of a number of studies, as these compounds are involved in a number of important inflammatory cell signaling mechanisms. Recent studies have further elucidated the role of MAPKs in the inflammatory response, as a result of trauma and/or ischemia–reperfusion (I/R) injury. There are three major classes of MAPKs that may be involved in the inflammatory response: extracellular signal-regulated kinases (ERKs), stress-activated protein kinases (SAPKs)/c-Jun NH2-terminal kinases (JNKs), and p38 MAPKs (p38). This is clinically relevant, because these pathways may be a possible target for anti-inflammatory drug intervention. This review studies the role of MAPKs in trauma and/or I/R.
Regulation of cytomegalovirus late-gene expression: differential use of three start sites in the transcriptional activation of ICP36 gene expression

We have investigated the transcriptional regulation of the human cytomegalovirus gamma gene encoding the ICP36 family (p52, the major late DNA-binding protein). The ICP36 transcription unit initiates at three distinct sites which are separated by approximately 50 nucleotides and are differentially regulated during infection. At early times (8 h postinfection), only two of these start sites, the most proximal and distal site, were active whereas at late times (36 h postinfection), the middle start site was activated. Expression from this late start site was dependent upon DNA replication. Consensus TATA elements were located upstream of all three start sites, although the element upstream of the late start site was unusual in both sequence and position when compared with conventional TATA elements. Deletion analysis was used in conjunction with transient assays to define independent promoters in this region. The two early start sites and associated TATA elements functioned as separable independently regulated promoters. The region containing the late start site and TATA element but excluding either of the flanking TATA elements was inactive in transient assays. Our work establishes that the ICP36 gene is under complex early and late transcriptional regulation and that the sequences regulating transcriptional activation are temporally and spatially distinct.
Extracellular hydrogen peroxide, produced through a respiratory burst oxidase/superoxide dismutase pathway, directs ingrowth wall formation in epidermal transfer cells of Vicia faba cotyledons

The intricate, and often polarized, ingrowth walls of transfer cells (TCs) amplify their plasma membrane surface areas to confer a transport function of supporting high rates of nutrient exchange across apo-/symplasmic interfaces. The TC ingrowth wall comprises a uniform wall layer on which wall ingrowths are deposited. Signals and signal cascades inducing trans-differentiation events leading to formation of TC ingrowth walls are poorly understood. Vicia faba cotyledons offer a robust experimental model to examine TC induction as, when placed into culture, their adaxial epidermal cells rapidly (h) and synchronously form polarized ingrowth walls accessible for experimental observations. Using this model, we recently reported findings consistent with extracellular hydrogen peroxide, produced through a respiratory burst oxidase homolog/superoxide dismutase pathway, initiating cell wall biosynthetic activity and providing directional information guiding deposition of the polarized uniform wall. Our conclusions rested on observations derived from pharmacological manipulations of hydrogen peroxide production and correlative gene expression data sets. A series of additional studies were undertaken, the results of which verify that extracellular hydrogen peroxide contributes to regulating ingrowth wall formation and is generated by a respiratory burst oxidase homolog/superoxide dismutase pathway.
Response: An Interactive Study Technique

Although an array of useful techniques are available to encourage effective studying, this is an aspect of the learning process in which teacher and students typically do not interact. The teacher’s role is usually limited to providing instruction in study strategies, encouraging their use, and using the results of tests as feedback on the effectiveness of study.