Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering the Interplay between Two Independent Functions of the Small RNA Regulator SgrS in Salmonella

ABSTRACT Bacterial dual-function small RNAs regulate gene expression by RNA-RNA base pairing and also code for small proteins. SgrS is a dual-function small RNA in Escherichia coli and Salmonella that is expressed under stress conditions associated with accumulation of sugar-phosphates, and its activity is crucial for growth during stress. The base-pairing function of SgrS regulates a number of mRNA targets, resulting in reduced uptake and enhanced efflux of sugars. SgrS also encodes the SgrT protein, which reduces sugar uptake by a mechanism that is independent of base pairing. While SgrS base-pairing activity has been characterized in detail, little is known about how base pairing and translation of sgrT are coordinated. In the current study, we utilized a series of mutants to determine how translation of sgrT affected the efficiency of base pairing-dependent regulation and vice versa. Mutations that abrogated sgrT translation had minimal effects on base-pairing activity. Conversely, mutations that impaired base-pairing interactions resulted in increased SgrT production. Furthermore, while ectopic overexpression of sgrS mutant alleles lacking only one of the two functions rescued cell growth under stress conditions, the SgrS base-pairing function alone was indispensable for growth rescue when alleles were expressed from the native locus. Collectively, the results suggest that during stress, repression of sugar transporter synthesis via base pairing with sugar transporter mRNAs is the first priority of SgrS. Subsequently, SgrT is made and acts on preexisting transporters. The combined action of these two functions produces an effective stress response.
Algorithm 757: MISCFUN, a software package to compute uncommon special functions

MISCFUN (MISCellaneous FUNctions) is a Fortran package for the evaluation of several special functions, which are not used often enough to have been included in the standard libraries or packages. The package uses Chebyshev expansions as the underlying method of approximation, with the Chebyshev coefficients given to 20D. A wide variety of functions are included, and the package is designed so that other functions can be added in a standard manner.
Black cohosh (Cimicifuga racemosa) in tamoxifen-treated breast cancer patients with climacteric complaints – a prospective observational study

Objective. The antihormonal therapy of breast cancer patients with the antiestrogen tamoxifen often induces or aggravates menopausal complaints. As estrogen substitution is contraindicated, herbal alternatives, e.g. extracts of black cohosh are often used. Design. A prospective observational study was carried out in 50 breast cancer patients with tamoxifen treatment. All patients had had surgery, most of them had undergone radiation therapy (87%) and approximately 50% had received chemotherapy. Every patient was treated with an isopropanolic extract of black cohosh (1–4 tablets, 2.5 mg) for 6 months. Patients recorded their complaints before therapy and after 1, 3, and 6 months of therapy using the menopause rating scale (MRS II). Results. The reduction of the total MRS II score under black cohosh treatment from 17.6 to 13.6 was statistically significant. Hot flashes, sweating, sleep problems, and anxiety improved, whereas urogenital and musculoskeletal complaints did not change. In all, 22 patients reported adverse events, none of which were linked with the study medication; 90% reported the tolerability of the black cohosh extract as very good or good. Conclusions. Black cohosh extract seems to be a reasonable treatment approach in tamoxifen treated breast cancer patients with predominantly psychovegetative symptoms.
Acute Dialysis Quality Initiative (ADQI): Methodology

The Acute Dialysis Quality Initiative (ADQI) is an ongoing process that seeks to produce evidence-based recommendations for the prevention and management of acute kidney injury (AKI) and on different issues concerning acute dialysis. Our methods involve a combination of both expert panel and evidence appraisal, and this approach was chosen to achieve the best of both options. This approach has led to important practice guidelines with wide acceptance and adoption into clinical practice. We further recognize that additional research will be needed and have proposed specific studies that will help move this field forward.
Coincidence of ipsilateral ocular dominance peaks with orientation pinwheel centers in cat visual cortex

Geometrical relationships among multiple cortical maps, such as those between ocular dominance and orientation maps, are a prominent feature of the brain's functional architecture. It is also well known that there is a strong bias of cortical responses toward the contralateral eye during early postnatal development. We wondered therefore whether and how such an imbalance of cortical responsiveness in a developing animal might influence the mutual geometrical relationships between orientation and ocular dominance maps in adult animals. The results of our study indicate the existence of a strong tendency for the peaks of the ipsilateral eye domains to coincide with the location of point singularities (pinwheel centers) in orientation maps. No such relationship was found for the peaks of contralateral eye domains. Computational studies reproduced similar asymmetry in the coincidence under the contralateral eye bias of inputs. Our study raised the idea that the pinwheel centers play an important role for retaining the weaker ipsilateral eye inputs during normal development.
p21Waf1/Cip1 Inhibition of Cyclin E/Cdk2 Activity Prevents Endoreduplication after Mitotic Spindle Disruption

ABSTRACT During a normal cell cycle, entry into S phase is dependent on completion of mitosis and subsequent activation of cyclin-dependent kinases (Cdks) in G1. These events are monitored by checkpoint pathways. Recent studies and data presented herein show that after treatment with microtubule inhibitors (MTIs), cells deficient in the Cdk inhibitor p21Waf1/Cip1 enter S phase with a ≥4N DNA content, a process known as endoreduplication, which results in polyploidy. To determine how p21 prevents MTI-induced endoreduplication, the G1/S and G2/M checkpoint pathways were examined in two isogenic cell systems: HCT116 p21+/+ and p21−/− cells and H1299 cells containing an inducible p21 expression vector (HIp21). Both HCT116 p21−/− cells and noninduced HIp21 cells endoreduplicated after MTI treatment. Analysis of G1-phase Cdk activities demonstrated that the induction of p21 inhibited endoreduplication through direct cyclin E/Cdk2 regulation. The kinetics of p21 inhibition of cyclin E/Cdk2 activity and binding to proliferating-cell nuclear antigen in HCT116 p21+/+ cells paralleled the onset of endoreduplication in HCT116 p21−/− cells. In contrast, loss of p21 did not lead to deregulated cyclin D1-dependent kinase activities, nor did p21 directly regulate cyclin B1/Cdc2 activity. Furthermore, we show that MTI-induced endoreduplication in p53-deficient HIp21 cells was due to levels of p21 protein below a threshold required for negative regulation of cyclin E/Cdk2, since ectopic expression of p21 restored cyclin E/Cdk2 regulation and prevented endoreduplication. Based on these findings, we propose that p21 plays an integral role in the checkpoint pathways that restrain normal cells from entering S phase after aberrant mitotic exit due to defects in microtubule dynamics.
Periplasmic binding proteins as optical modulators of single-walled carbon nanotube fluorescence: amplifying a nanoscale actuator.

The authors use glucose-binding protein (GBP) to mech. actuate a fluorescent single-walled carbon nanotube (SWNT), resulting in reversible exciton quenching in response to glucose. The GBP is covalently conjugated with carboxylated poly(vinyl alc.)-wrapped SWNTs (cPVA/SWNTs), which leads to allosterically controlled optical transduction in response to glucose. Carboxy groups on the cPVA/SWNT complex were used to attach the protein, through amine coupling to lysine residues on the GBP. These complexes demonstrate a reversible fluorescence quenching in response to glucose. The hypothesis is that the hinge bending action assocd. with glucose recognition modulates the fluorescence of the SWNT. The system can be used as a glucose biosensor. [on SciFinder(R)]
AN ALGORITHM FOR CREATING GROOVE TEMPLATES FOR APPLICATION TO MIDI DRUM DATA

A method of characterizing the timing and amplitude tendencies of percussive onsets in drum audio tracks is introduced. The method uses a variety of existing high performance algorithms for onset detection, tempo estimation, and source separation along with some original modifications to accomplish the desired task. An emphasis is placed on drum audio track for popular music, in which the source instruments originate from a standard drum kit. The timing and amplitude tendencies of the audio are modelled with normal distribution functions for each beat subdivision and then used to generate timing and velocity shifts for programmed MIDI drum tracks.
Estimación y aplicación de medidas de confianza en reconocimiento automático del habla

En esta tesis se aborda el problema de la estimacion y aplicacion de medidas de confianza en reconocimiento automatico del habla. Este problema es una de las lineas de investigacion abiertas dentro del reconocimiento del habla y, en los ultimos anos, ha desperado un crecimiento interes por su utilidad. El objetivo es medir la fiabilidad de las palabras producto del reconocimiento, y detectar aquellas que sean susceptibles de ser errores. En la tesis este problema se aborda como un problema clasico de clasificacion en dos clases: correcta e incorrecta. Para ello, cada palabra se representa por un conjunto de caracteristicas y, utilizando tecnicas conocidas del reconocimiento de formas, se clasifica en una de las dos posibles clases. El trabajo de investigacion se centra en dos frentes; por una parte, encontrar nuevas caracteristicas que aporten informacion util sobre la correccion de las palabras reconocidas, y por otra, definir un clasificador, dentro del marco estadistico, que obtenga resultados satisfactorios en la estimacion de la medida de confianza. Se proponen cuatro nuevas caracteristicas, las cuales se inspiran en observaciones que han sido utilizadas por otros autores. Una de ellas se basa en la variacion de uno de los parametros del reconocedor, denominado Grammar Scale Factor, y las otras tres se basan en la utilizacion de grafos de palabras. Asi mismo, se propone una mejora computacional que trata de resolver el principal inconveniente de una de las caracteristicas mas utiles que aparecen en la literatura: Acoustic Stability. Respecto al clasificador, se adoptan dos modelos diferentes: el primero, es una de las aportaciones de la tesis, y consiste en un modelo probabilistico dependiente de la palabra, que estima la medida de confianza mediante la combinacion naive Bayes de caracteristicas. Para tratar con el problema de escasez de datos de entrenamiento, el modelo se suaviza, utilizando t
Technical parameters of immunostaining of osmicated tissue in epoxy sections.

The development of the labeled and unlabeled antibody enzyme methods and their application at the light and electron microscopic level have led to the widespread use of postembedding staining techniques of a wide variety of antigens. An important step in the postembedding staining technique is the “etching” or pretreatment of the plastic section with an agent to enhance the binding of specific primary antibody to antigen in the section. Sodium ethoxide (14) or alcoholic sodium hydroxide (8) both of which physically dissolve polymerized epoxy resin, were initially used to facilitate tinctorial staining (8, 14) and later by Lange (9, 10) to enhance the immunofluorescence for glucagon in plastic sections of pancreatic islets. Hydrogen peroxide has been used to bleach osmium from plastic sections and to enhance staining for glycoproteins at the ultrastructural level (13, 15, 19), but was first used by Nakane (18) in 1971 to enhance immunostaining at the ultrastructural level for growth hormone and prolactin in osmicated sections of rat pituitary. Using the unlabeled antibody enzyme method, Moriarty and Halmi (17) and Erlandsen et al. (5) showed that intensity of immunostaining in the postembedding technique was enhanced if sections of aldehyde fixed tissue were briefly exposed to hydrogen peroxide before application of immunoreagents. The successful use of hydrogen peroxide and alcoholic sodium hydroxide in the enhancement of immunostaining has led to their widespread adoption as an essential step in postembedding staining despite the fact that there is relatively little information available as to what effect these agents may have on the plastic resin or on the stability and extraction of antigens from the tissue sections. In this report the effect of various types of “etching” or pretreatment agents on the surface topography of the plastic sections has been investigated and has been correlated with the immunostaining for lysozyme within rat Paneth cells and with the extraction of Na’25! by these agents from cured epoxy resin.
Extracorporeal shock wave therapy (ESWT) for wound healing: Technology, mechanisms, and clinical efficacy

For almost 30 years, extracorporeal shock wave therapy has been clinically implemented as an effective treatment to disintegrate urinary stones. This technology has also emerged as an effective noninvasive treatment modality for several orthopedic and traumatic indications including problematic soft tissue wounds. Delayed/nonhealing or chronic wounds constitute a burden for each patient affected, significantly impairing quality of life. Intensive wound care is required, and this places an enormous burden on society in terms of lost productivity and healthcare costs. Therefore, cost‐effective, noninvasive, and efficacious treatments are imperative to achieve both (accelerated and complete) healing of problematic wounds and reduce treatment‐related costs. Several experimental and clinical studies show efficacy for extracorporeal shock wave therapy as means to accelerate tissue repair and regeneration in various wounds. However, the biomolecular mechanism by which this treatment modality exerts its therapeutic effects remains unclear. Potential mechanisms, which are discussed herein, include initial neovascularization with ensuing durable and functional angiogenesis. Furthermore, recruitment of mesenchymal stem cells, stimulated cell proliferation and differentiation, and anti‐inflammatory and antimicrobial effects as well as suppression of nociception are considered important facets of the biological responses to therapeutic shock waves. This review aims to provide an overview of shock wave therapy, its history and development as well as its current place in clinical practice. Recent research advances are discussed emphasizing the role of extracorporeal shock wave therapy in soft tissue wound healing.
Polarity and Specific Sequence Requirements of Peroxisome Proliferator-activated Receptor (PPAR)/Retinoid X Receptor Heterodimer Binding to DNA

The malic enzyme (ME) gene is a target for both thyroid hormone receptors and peroxisome proliferator-activated receptors (PPAR). Within the ME promoter, two direct repeat (DR)-1-like elements, MEp and MEd, have been identified as putative PPAR response elements (PPRE). We demonstrate that only MEp and not MEd is able to bind PPAR/retinoid X receptor (RXR) heterodimers and mediate peroxisome proliferator signaling. Taking advantage of the close sequence resemblance of MEp and MEd, we have identified crucial determinants of a PPRE. Using reciprocal mutation analyses of these two elements, we show the preference for adenine as the spacing nucleotide between the two half-sites of the PPRE and demonstrate the importance of the two first bases flanking the core DR1 in 5′. This latter feature of the PPRE lead us to consider the polarity of the PPAR/RXR heterodimer bound to its cognate element. We demonstrate that, in contrast to the polarity of RXR/TR and RXR/RAR bound to DR4 and DR5 elements respectively, PPAR binds to the 5′ extended half-site of the response element, while RXR occupies the 3′ half-site. Consistent with this polarity is our finding that formation and binding of the PPAR/RXR heterodimer requires an intact hinge T region in RXR while its integrity is not required for binding of the RXR/TR heterodimer to a DR4.
Diagnostic accuracy of CD4 cell count increase for virologic response after initiating highly active antiretroviral therapy

Objective:To derive and internally validate a clinical prediction rule for virologic response based on CD4 cell count increase after initiation of HAART in a resource-limited setting. Design and methods:A retrospective cohort study at two HIV care clinics in Gaborone, Botswana. The participants were previously treatment-naive HIV-1-infected individuals initiating HAART. The main outcome measure was a plasma HIV-1 RNA level (viral load) ≤ 400 copies/ml (i.e. undetectable) 6 months after initiating HAART. Results:The ability of CD4 cell count increase to predict an undetectable viral load was significantly better in those with baseline CD4 cell counts ≤ 100 cells/μl [area under the ROC curve (AUC), 0.78; 95% confidence interval (CI), 0.67–0.89; versus AUC, 0.60; 95% CI, 0.48–0.71; P = 0.018]. The sensitivity, specificity, and positive and negative predictive values of a CD4 cell count increase of ≥ 50 cells/μl for an undetectable viral load in those with baseline CD4 cell counts ≤ 100 cells/μl were 93.1, 61.3, 92.5 and 63.3%, respectively. Alternatively, these values were 47.8, 87.1, 95.0 and 24.5%, respectively, if a increase in CD4 cell count of ≥ 150 cells/μl was used. Conclusions:CD4 cell count increase after initiating HAART has only moderate discriminative ability in identifying patients with an undetectable viral load, and the predictive ability is lower in patients with lower baseline CD4 cell counts. Although HIV treatment programs in resource-constrained settings could consider the use of CD4 cell count increases to triage viral load testing, more accurate approaches to monitoring virologic failure are urgently needed.
Coq6 Is Responsible for the C4-deamination Reaction in Coenzyme Q Biosynthesis in Saccharomyces cerevisiae*

Background: A deamination reaction is necessary for yeast to synthesize coenzyme Q from para-aminobenzoic acid. Results: The deamination requires dioxygen and an active Coq6 enzyme. Conclusion: The flavin monooxygenase Coq6 is responsible for the substitution of the amino group with a hydroxyl group. Significance: Coq6 hydroxylates two positions of its amino substrate and partly determines whether an organism can synthesize coenzyme Q from para-aminobenzoic acid. The yeast Saccharomyces cerevisiae is able to use para-aminobenzoic acid (pABA) in addition to 4-hydroxybenzoic acid as a precursor of coenzyme Q, a redox lipid essential to the function of the mitochondrial respiratory chain. The biosynthesis of coenzyme Q from pABA requires a deamination reaction at position C4 of the benzene ring to substitute the amino group with an hydroxyl group. We show here that the FAD-dependent monooxygenase Coq6, which is known to hydroxylate position C5, also deaminates position C4 in a reaction implicating molecular oxygen, as demonstrated with labeling experiments. We identify mutations in Coq6 that abrogate the C4-deamination activity, whereas preserving the C5-hydroxylation activity. Several results support that the deletion of Coq9 impacts Coq6, thus explaining the C4-deamination defect observed in Δcoq9 cells. The vast majority of flavin monooxygenases catalyze hydroxylation reactions on a single position of their substrate. Coq6 is thus a rare example of a flavin monooxygenase that is able to act on two different carbon atoms of its C4-aminated substrate, allowing its deamination and ultimately its conversion into coenzyme Q by the other proteins constituting the coenzyme Q biosynthetic pathway.
Lexicons on Demand: Neural Word Embeddings for Large-Scale Text Analysis

Human language is colored by a broad range of topics, but existing text analysis tools only focus on a small number of them. We present Empath, a tool that can generate and validate new lexical categories on demand from a small set of seed terms (like "bleed" and "punch" to generate the category violence). Empath draws connotations between words and phrases by learning a neural embedding across billions of words on the web. Given a small set of seed words that characterize a category, Empath uses its neural embedding to discover new related terms, then validates the category with a crowd-powered filter. Empath also analyzes text across 200 built-in, pre-validated categories we have generated such as neglect, government, and social media. We show that Empath's data-driven, human validated categories are highly correlated (r=0.906) with similar categories in LIWC.
Diagnostic value of additional 68Ga-PSMA-PET before 223Ra-dichloride therapy in patients with metastatic prostate carcinoma

Summary Purpose: Medical imaging plays an important role in selecting patients with metastatic castration-resistant prostate cancer for 223Ra- dichloride therapy of bone metastases. The purpose of this study was to investigate whether 68Ga-PSMA-PET has incremental value over conventional imaging for selecting patients suitable for 223Ra-dichloride therapy. Methods: In 27 consecutive patients referred for 223Ra-dichloride therapy additional 68Ga-PSMA-PET/CT was performed and tracer distribution was evaluated systematically with respect to the detection of visceral metastases and bone metastases with inadequate uptake on bone scintigraphy. Results: In 4 patients (15 %) 68Ga- PSMA-PET revealed previously unknown visceral metastases (3 liver, 1 adrenal gland), which changed the therapeutic decision in 2 cases. PET revealed more extended tumour involvement in the bone compared to bone scintigraphy in 9 patients (33 %). In 3 of these, the mismatch was extensive enough to question suitability for 223Ra-dichloride therapy. Conclusions: Additional 68Ga-PSMA-PET as a gatekeeper between conventional staging and 223Ra-dichloride therapy can provide valuable additional information with regard to visceral metastases and tumour manifestations without adequate bone mineral turnover. It may lead to a change in therapeutic management in a significant number of patients and should therefore be considered in future clinical trials.
Multirobot Cooperative Learning for Semiautonomous Control in Urban Search and Rescue Applications

The use of cooperative multirobot teams in urban search and rescue (USAR) environments is a challenging yet promising research area. For multirobot teams working in USAR missions, the objective is to have the rescue robots work effectively together to coordinate task allocation and task execution between different team members in order to minimize the overall exploration time needed to search disaster scenes and to find as many victims as possible. This paper presents the development of a multirobot cooperative learning approach for a hierarchical reinforcement learning (HRL) based semiautonomous control architecture in order to enable a robot team to learn cooperatively to explore and identify victims in cluttered USAR scenes. The proposed cooperative learning approach allows effective task allocation among the multirobot team and efficient execution of the allocated tasks in order to improve the overall team performance. Human intervention is requested by the robots when it is determined that they cannot effectively execute an allocated task autonomously. Thus, the robot team is able to make cooperative decisions regarding task allocation between different team members (robots and human operators) and to share experiences on execution of the allocated tasks. Extensive results verify the effectiveness of the proposed HRL‐based methodology for multi‐robot cooperative exploration and victim identification in USAR‐like scenes.