Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple Mechanisms of Suppression Circumvent Transcription Defects in an RNA Polymerase Mutant

ABSTRACT Using a high-copy-number suppressor screen to obtain clues about the role of the yeast RNA polymerase II subunit RPB4 in transcription, we identified three suppressors of the temperature sensitivity resulting from deletion of the RPB4 gene (ΔRPB4). One suppressor is Sro9p, a protein related to La protein, another is the nucleosporin Nsp1p, and the third is the RNA polymerase II subunit RPB7. Suppression by RPB7 was anticipated since its interaction with RPB4 is well established both in vitro and in vivo. We examined the effect of overexpression of each suppressor gene on transcription. Interestingly, suppression of the temperature-sensitive phenotype correlates with the correction of a characteristic transcription defect of this mutant: each suppressor restored the level of promoter-specific, basal transcription to wild-type levels. Examination of the effects of the suppressors on other in vivo transcription aberrations in ΔRPB4 cells revealed significant amelioration of defects in certain inducible genes in Sro9p and RPB7, but not in Nsp1p, suppressor cells. Analysis of mRNA levels demonstrated that overexpression of each of the three suppressors minimally doubled the mRNA levels during stationary phase. However, the elevated mRNA levels in Sro9p suppressor cells appear to result from a combination of enhanced transcription and message stability. Taken together, these results demonstrate that these three proteins influence transcription and implicate Sro9p in both transcription and posttranscription events.
Streaming compression of tetrahedral volume meshes

Geometry processing algorithms have traditionally assumed that the input data is entirely in main memory and available for random access. This assumption does not scale to large data sets, as exhausting the physical memory typically leads to IO-inefficient thrashing. Recent works advocate processing geometry in a "streaming" manner, where computation and output begin as soon as possible. Streaming is suitable for tasks that require only local neighbor information and batch process an entire data set.We describe a streaming compression scheme for tetrahedral volume meshes that encodes vertices and tetrahedra in the order they are written. To keep the memory footprint low, the compressor is informed when vertices are referenced for the last time (i.e. are finalized). The compression achieved depends on how coherent the input order is and how many tetrahedra are buffered for local reordering. For reasonably coherent orderings and a buffer of 10,000 tetrahedra, we achieve compression rates that are only 25 to 40 percent above the state-of-the-art, while requiring drastically less memory resources and less than half the processing time.
Lysogenic Conversion of the Phytopathogen Ralstonia solanacearum by the P2virus ϕRSY1

A P2-like phage ϕRSY1 infecting the phytopathogen Ralstonia solanacearum was isolated and characterized. The 40-kb genome of ϕRSY1 showed high sequence similarity to the Ralstonia phage ϕRSA1 and the GMI1000 prophage ϕRSX. The major genomic differences between these phages were the different orientation of the int gene and the gene content close to the cosL. ϕRSY1 and ϕRSX use a 15-base 3′ portion of the serine tRNA(GGA) gene as attB, while ϕRSA1 uses a 45-base 3′ portion of the arginine tRNA(CCG) gene. The different orientation of int in the genomes means that the gene arrangements in the prophage states are reversed in ϕRSY1 and ϕRSA1. Several putative gene products of ϕRSY1 may affect the bacterium’s fitness. ϕRSY1 contains an open reading frame (ORF) that seems to encode a protein similar to Vgr in the type VI secretion system of various bacterial species. ϕRSY1 lysogens showed phenotypic changes including enhanced twitching motility, large colony formation, and easy aggregation of cells, suggesting involvement of this ORF in the changes. In view of these phage gene arrangements, we surveyed prophages in the genomes of various R. solanacearum strains and found that the P2-like phages of R. solanacearum (14 phages) consist of two major groups: the ϕRSY1-type and the ϕRSA1-type. The relationships and evolution of these P2-like phages inferred from our data are discussed in detail.
Cued Recall and the Nature of the Memory Disorder in Dementia

Summary The study investigated the retrieval deficit hypothesis of forgetting in senile dementia, using a cued recall technique. Memory for lists of words was tested with either no cues given at the time of recall, or alternatively by cueing the patient either with the word's first letter or its semantic category. Results do not support a retrieval deficit explanation of forgetting in dementia, but instead suggest the possibility of a processing deficit at the acquisition stage.
Reproductive biology of female titi monkeys (Callicebus moloch) in captivity

Titi monkeys (Callicebus spp., Cebidae) are monogamous neotropical primates that live in family‐like groups typically consisting of an adult monogamous pair and one or two young. Knowledge about the reproductive biology of this genus is scanty. This study investigated the reproductive biology of female dusky titi monkeys (Callicebus moloch). An initial analysis characterized reproductive parameters of 32 females from a captive colony maintained for 23 years at the California Regional Primate Research Center (CRPRC). The colony records provided data on reproductive parameters such as interbirth intervals, seasonality, age at first pregnancy, and reproductive rate in captivity. Changes in urinary levels of estrone conjugates (E1C) and pregnanediol‐3alpha‐glucuronide (PdG) were used to characterize major reproductive events. Urine samples from eleven females were collected during 17 months. The endocrine data were used to examine changes associated with cycling, conception, and the post‐partum period as well as to determine the duration of the ovarian cycle and gestation length. The analysis of colony records indicated that females whose infant survived through weaning gave birth at intervals remarkably close to one year, while those who lost their offspring showed a significantly shorter interval. As long as they lived within the family group, mature female offspring did not breed. The analysis of the endocrine profiles indicated that after giving birth to a viable offspring, females undergo a relatively prolonged period of anovulation (approx. 6.5 months), followed by 1‐3 non‐conceptive cycles (approx. 1 month), after which they conceive and gestate (4.3 months). Am. J. Primatol. 47:183–195, 1999. © 1999 Wiley‐Liss, Inc.
Robust texture features for blurred images using Undecimated Dual-Tree Complex Wavelets

This paper presents a new descriptor for texture classification. The descriptor is rotationally invariant and blur insensitive, which provides great benefits for various applications that suffer from out-of-focus content or involve fast moving or shaking cameras. We employ an Undecimated Dual-Tree Complex Wavelet Transform (UDT-CWT) [1] to extract texture features. As the UDT-CWT fully provides local spatial relationship between scales and subband orientations, we can straightforwardly create bit-planes of the images representing local phases of wavelet coefficients. We also discard some of the finest decomposition levels where are most affected by the blur. A histogram of the resulting code words is created and used as features in texture classification. Experimental results show that our approach outperforms existing methods by up to 40% for synthetic blurs and up to 30% for natural video content due to camera motion when walking.
Using stranger as sensors: temporal and geo-sensitive question answering via social media

MoboQ is a location-based real-time social question answering service deployed in the field in China. Using MoboQ, people can ask temporal and geo-sensitive questions, such as how long is the line at a popular business right now, and then receive answers that crowdsourced from other users in a timely fashion. To obtain answers for questions, the system analyzes the live stream from public microblogging service Sina Weibo to identify people who are likely to currently be at the place that is associated with a question and sends them the unsolicited question through the microblogging service from which they were identified. MoboQ was deployed in China at the beginning of 2012, until October of the same year, it was used to ask 15,224 questions by 35,214 registered users, and it gathered 29,491 answers; 74.6% of the questions received at least one answer, 28% received a first response within 10 minutes, and 51% of the questions got first answer within 20 minutes. In total, 91% of the questions successfully found at least one answer candidate, and they were sent to 162,954 microblogging service users. We analyze the usage patterns and behaviors of the real-world end-users, discuss the lessons learned, and outline the future directions and possible applications that could be built on top of MoboQ.
Transcription-coupled deposition of histone modifications during MHC class II gene activation

Posttranslational histone modifications associated with actively expressed genes are generally believed to be introduced primarily by histone-modifying enzymes that are recruited by transcription factors or their associated co-activators. We have performed a comprehensive spatial and temporal analyses of the histone modifications that are deposited upon activation of the MHC class II gene HLA-DRA by the co-activator CIITA. We find that transcription-associated histone modifications are introduced during two sequential phases. The first phase precedes transcription initiation and is characterized exclusively by a rapid increase in histone H4 acetylation over a large upstream domain. All other modifications examined, including the acetylation and methylation of several residues in histone H3, are restricted to short regions situated at or within the 5′ end of the gene and are established during a second phase that is concomitant with ongoing transcription. This second phase is completely abrogated when elongation by RNA polymerase II is blocked. These results provide strong evidence that transcription elongation can play a decisive role in the deposition of histone modification patterns associated with inducible gene activation.
Analysis of Tub4p, a yeast gamma-tubulin-like protein: implications for microtubule-organizing center function

gamma-Tubulin is a conserved component of microtubule-organizing centers and is thought to be involved in microtubule nucleation. A recently discovered Saccharomyces cerevisiae gene (TUB4) encodes a tubulin that is related to, but divergent from, gamma-tubulins. TUB4 is essential for cell viability, and epitope-tagged Tub4 protein (Tub4p) is localized to the spindle pole body (Sobel, S.G., and M. Snyder. 1995.J. Cell Biol. 131:1775-1788). We have characterized the expression of TUB4, the association of Tub4p with the spindle pole body, and its role in microtubule organization. Tub4p is a minor protein in the cell, and expression of TUB4 is regulated in a cell cycle-dependent manner. Wild-type Tub4p is localized to the spindle pole body, and a Tub4p- green fluorescent protein fusion is able to associate with a preexisting spindle pole body, suggesting that there is dynamic exchange between cytoplasmic and spindle pole body forms of Tub4p. Perturbation of Tub4p function, either by conditional mutation or by depletion of the protein, results in spindle as well as spindle pole body defects, but does not eliminate the ability of microtubules to regrow from, or remain attached to, the spindle pole body. The spindle pole bodies in tub4 mutant cells duplicate but do not separate, resulting in a monopolar spindle. EM revealed that one spindle pole body of the duplicated pair appears to be defective for the nucleation of microtubules. These results offer insight into the role of gamma- tubulin in microtubule-organizing center function.
A Small Interfering RNA Targeting Coxsackievirus B3 Protects Permissive HeLa Cells from Viral Challenge

ABSTRACT We examined the ability of small interfering RNAs (siRNAs) to disrupt infection by coxsackievirus B3 (CVB3). The incorporation of siRNAs dramatically decreased cell death in permissive HeLa cells in parallel with a reduction in viral replication. Three of four siRNAs had potent anti-CVB3 activity. The present study thus demonstrates that the antiviral effect is due to the downregulation of viral replication. In addition, an effective CVB3-specific siRNA had similar antiviral effects in other related enteroviruses possessing sequence homology in the targeted region. Because the CVB3-specific siRNA is effective against other enteroviruses, siRNAs have potential for a universal antienterovirus strategy.
Pulsatile tinnitus.

Pulse-synchronous tinnitus suggests a vascular etiology and is deemed rare by the otologic literature. During the period 1978-1985 we evaluated 20 patients with the sole or initial complaint of pulsatile tinnitus. Fourteen patients had objective pulsatile tinnitus, perceived by the patient and the examiner alike, and 6 had subjective pulsatile tinnitus, perceived by the patient only. Angiographic findings in patients with objective pulsatile tinnitus included dural or pial arteriovenous malformations, occlusive disease of the intra- or extracranial carotid arteries from atherosclerosis or dissection, panarterial ectasia, and venous sinus thrombosis. Most of the patients with subjective pulsatile tinnitus had normal evaluations, but other possible causes of subjective pulsatile tinnitus included a carotid occlusion and pseudotumor cerebri. Pulsatile tinnitus is an uncommon symptom produced by a variety of causes. Given the abnormalities present in our series, we would recommend intraarterial digital subtraction angiography or conventional angiography in the evaluation of objective pulsatile tinnitus and intravenous digital subtraction angiography for subjective pulsatile tinnitus. Increased intracranial pressure must also be considered.
Recognition of Linear Context-Free Rewriting Systems

The class of linear context-free rewriting systems has been introduced as a generalization of a class of grammar formalisms known as mildly context-sensitive. The recognition problem for linear context-free rewriting languages is studied at length here, presenting evidence that, even in some restricted cases, it cannot be solved efficiently. This entails the existence of a gap between, for example, tree adjoining languages and the subclass of linear context-free rewriting languages that generalizes the former class; such a gap is attributed to "crossing configurations". A few other interesting consequences of the main result are discussed, that concern the recognition problem for linear context-free rewriting languages.
Actions of melatonin mixed with collagenized porcine bone versus porcine bone only on osteointegration of dental implants

Abstract: This study evaluated the effect of the topical application of melatonin mixed with collagenized porcine bone on the osteointegration on the rough discrete calcium deposit (DCD) surface implants in Beagle dogs 3 months after their insertion. In preparation for subsequent insertion of dental implants, lower molars were extracted from 12 Beagle dogs. Each mandible received two parallel wall expanded platform implants with a DCD surface of 4 mm in diameter and 10 mm in length. The implants were randomly assigned to the distal sites on each mandible in the molar area and the gaps were filled with 5 mg lyophilized powdered melatonin and porcine bone and collagenized porcine bone alone. Ten histological sections per implant were obtained for histomorphometric studies. After a 4‐wk treatment period, melatonin plus porcine bone significantly increased the perimeter of bone that was in direct contact with the treated implants (P < 0.0001), bone density (P < 0.0001), and new bone formation (P < 0.0001) in comparison with porcine bone alone around the implants. Melatonin plus collagenized porcine bone on DCD surface may act as a biomimetic agent in the placement of endo‐osseous dental implants and enhance the osteointegration. Melatonin combined with porcine bone on DCD implants reveals more bone in implant contact at 12 wk (84.5 ± 1.5%) compared with porcine bone alone treated area (67.17 ± 1.2%).
Cytokines as genetic modifiers in K5–/– mice and in human epidermolysis bullosa simplex

Epidermolysis bullosa simplex (EBS) is a skin disorder caused by fully‐penetrant mutations in the keratin genes KRT5 and KRT14, leading to extensive cytolysis and cell fragility of basal keratinocytes. EBS is subject to environmental conditions and displays high intra‐ and interfamilial variability, suggesting modifying loci. Here, we demonstrate that upregulation of certain cytokines accompanies mutations in keratin 5 (K5) but not in keratin 14 (K14). We find for the first time that cytokines macrophage chemotactic protein (MCP)‐1/[chemokine (C‐C motif) ligand 2] (CCL2), macrophage inflammatory protein (MIP)‐3β/CCL19 and MIP‐3α/CCL20, all regulated by nuclear factor kappa B (NFκB) and involved in the recruitment, maturation, and migration of Langerhans cells (LCs) in the epidermis, are upregulated in the skin of K5–/–, but not of K14–/– mice. In neonatal K5–/– epidermis, the number of LCs was increased two‐fold. At the same time, tumor necrosis factor alpha (TNFα) remained unaltered, demonstrating the specificity of that process. Most remarkably, enhanced LC recruitment within the epidermis was found in five EBS patients carrying mutations in the KRT5 gene but not in EBS patients with KRT14 gene mutations. In agreement with the NFκB‐dependent regulation of these cytokines, we found a decrease in p120‐catenin in the basal epidermis of K5–/– mice. These data provide the first explanation for distinct, keratin‐type‐specific genotype–phenotype correlations in EBS and represent a rationale to investigate gene loci affecting skin pathology in EBS. Hum Mutat 0, 1–10, 2009. © 2009 Wiley‐Liss, Inc.
Visual speech features representation for automatic lip-reading

A fundamental task in the pattern recognition field is to find a suitable representation for a feature. We present a new visual speech feature representation approach that combines hypercolumn model (HCM) with HMM to perform a complete lip-reading system. We use HCM to extract visual speech features from the input image. The extracted features are modeled by Gaussian distributions using HMM. The proposed lip-reading system can work under varying lip positions and sizes. All images were captured in a natural environment without using special lighting or lip markers. Experimental results are shown to compare favourably with the results of two reported systems, SOM and DCT based systems. HCM provides better performance than both of these systems.
Exercise Training and Beta-Alanine-Induced Muscle Carnosine Loading

Purpose Beta-alanine (BA) supplementation has been shown to augment muscle carnosine concentration, thereby promoting high-intensity (HI) exercise performance. Trained muscles of athletes have a higher increase in carnosine concentration after BA supplementation compared to untrained muscles, but it remains to be determined whether this is due to an accumulation of acute exercise effects or to chronic adaptations from prior training. The aim of the present study was to investigate whether high-volume (HV) and/or HI exercise can improve BA-induced carnosine loading in untrained subjects. Methods All participants (n = 28) were supplemented with 6.4 g/day of BA for 23 days. The subjects were allocated to a control group, HV, or HI training group. During the BA supplementation period, the training groups performed nine exercise sessions, consisting of either 75–90 min continuous cycling at 35–45% Wmax (HV) or 3 to 5 repeats of 30 s cycling at 165% Wmax with 4 min recovery (HI). Carnosine content was measured in soleus and gastrocnemius medialis by proton magnetic resonance spectroscopy. Results There was no difference in absolute increase in carnosine content between the groups in soleus and gastrocnemius muscle. For the average muscle carnosine content, a higher absolute increase was found in HV (+2.95 mM; P = 0.046) and HI (+3.26 mM; P = 0.028) group compared to the control group (+1.91 mM). However, there was no additional difference between the HV and HI training group. Conclusion HV and HI exercise training showed no significant difference on BA-induced muscle carnosine loading in soleus and gastrocnemius muscle. It can be suggested that there can be a small cumulative effect of exercise on BA supplementation efficiency, although differences did not reach significance on individual muscle level.
Spectral Estimation of Nonstationary EEG Using Particle Filtering With Application to Event-Related Desynchronization (ERD)

This paper proposes non-Gaussian models for parametric spectral estimation with application to event-related desynchronization (ERD) estimation of nonstationary EEG. Existing approaches for time-varying spectral estimation use time-varying autoregressive (TVAR) state-space models with Gaussian state noise. The parameter estimation is solved by a conventional Kalman filtering. This study uses non-Gaussian state noise to model autoregressive (AR) parameter variation with estimation by a Monte Carlo particle filter (PF). Use of non-Gaussian noise such as heavy-tailed distribution is motivated by its ability to track abrupt and smooth AR parameter changes, which are inadequately modeled by Gaussian models. Thus, more accurate spectral estimates and better ERD tracking can be obtained. This study further proposes a non-Gaussian state space formulation of time-varying autoregressive moving average (TVARMA) models to improve the spectral estimation. Simulation on TVAR process with abrupt parameter variation shows superior tracking performance of non-Gaussian models. Evaluation on motor-imagery EEG data shows that the non-Gaussian models provide more accurate detection of abrupt changes in alpha rhythm ERD. Among the proposed non-Gaussian models, TVARMA shows better spectral representations while maintaining reasonable good ERD tracking performance.
Managing stress urinary incontinence – a primary care issue

Stress urinary incontinence (SUI) is a common condition in women, caused by anatomical problems related to factors such as age, parity, menopause and obesity. Depending on the clinical findings and on the severity of symptoms, SUI can be managed with conservative methods including pelvic floor exercises, vaginal cones and general lifestyle modification advice; or, it can be treated surgically with procedures such as Burch colposuspension, vaginal slings or tension‐free tapes and injection of bulking agents alongside the urethra. SUI is greatly underdiagnosed, because many women are reluctant to consult their doctors about their condition. Department of Health guidelines are placing greater emphasis on primary care management of the condition and Primary Care Trusts (PCTs) to provide consistent, integrated continence care services. The availability of new, non‐invasive treatment options, such as duloxetine, are likely to have a positive impact on the future of SUI management.