Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of a photometric method with standardized methods of antifungal susceptibility testing of yeasts

We determined the fluconazole MICs for 101 clinical isolates of Candida and Cryptococcus neoformans using the macro- and microdilution methods recommended by the National Committee for Clinical Laboratory Standards. We compared the MICs obtained by these methods with those obtained by a photometric assay that quantified the reduction of 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) by viable fungi. The MIC determined by this method was defined as the highest fluconazole concentration associated with the first precipitous drop in optical density. For Candida, both the MTT and the microdilution methods demonstrated excellent agreement with the standard macrodilution method. The MTT method, however, generated MICs at 24 h that were comparable to those generated by the standard macrodilution method, whereas the microdilution method required 48 h. For C. neoformans, the levels of agreement between the MICs determined by the MTT and microdilution methods after 48 h and those determined by the standard 72-h macrodilution method were 94% (29 of 31) and 94% (29 of 31), respectively. The MTT method therefore provided results comparable to those of currently recommended methods and had the advantages of a more rapid turnaround time and potential adaptability to use as an automated system. Furthermore, the MICs determined by the MTT method were determined photometrically, thereby eliminating reader bias.
Fatty acid DSF binds and allosterically activates histidine kinase RpfC of phytopathogenic bacterium Xanthomonas campestris pv. campestris to regulate quorum-sensing and virulence

As well as their importance to nutrition, fatty acids (FA) represent a unique group of quorum sensing chemicals that modulate the behavior of bacterial population in virulence. However, the way in which full-length, membrane-bound receptors biochemically detect FA remains unclear. Here, we provide genetic, enzymological and biophysical evidences to demonstrate that in the phytopathogenic bacterium Xanthomonas campestris pv. campestris, a medium-chain FA diffusible signal factor (DSF) binds directly to the N-terminal, 22 amino acid-length sensor region of a receptor histidine kinase (HK), RpfC. The binding event remarkably activates RpfC autokinase activity by causing an allosteric change associated with the dimerization and histidine phosphotransfer (DHp) and catalytic ATP-binding (CA) domains. Six residues were found essential for sensing DSF, especially those located in the region adjoining to the inner membrane of cells. Disrupting direct DSF-RpfC interaction caused deficiency in bacterial virulence and biofilm development. In addition, two amino acids within the juxtamembrane domain of RpfC, Leu172 and Ala178, are involved in the autoinhibition of the RpfC kinase activity. Replacements of them caused constitutive activation of RpfC-mediated signaling regardless of DSF stimulation. Therefore, our results revealed a biochemical mechanism whereby FA activates bacterial HK in an allosteric manner, which will assist in future studies on the specificity of FA-HK recognition during bacterial virulence regulation and cell-cell communication.
The cdk inhibitor p27Xic1 is required for differentiation of primary neurones in Xenopus

We have investigated the role of the cyclin-dependent kinase inhibitor, p27Xic1, in the coordination of cell cycle exit and differentiation during early neurogenesis. We demonstrate that p27Xic1 is highly expressed in cells destined to become primary neurones and is essential for an early stage of neurogenesis. Ablation of p27Xic1 protein prevents differentiation of primary neurones, while overexpressing p27Xic1 promotes their formation. p27Xic1 may enhance neurogenesis by stabilising the bHLH protein, neurogenin. Moreover, the ability of p27Xic1 to stabilise neurogenin and enhance neurogenesis localises to an N-terminal domain of the molecule and is separable from its ability to inhibit the cell cycle.
Transmit beamforming and admission control for multicast with uncertain user partition

In this paper, we consider the multicast beamforming problem in a downlink wireless system. Then, an optimization problem is formulated to find the optimal user-group assignment scheme and beamforming weight vectors, such that the number of admitted users is maximized with the minimum transmit power under the quality of service (QoS) requirement constraints of each individual user. Unfortunately, the constraints are nonlinear since they consist of the products of binary variables and continuous variables. As a solution, the big-M approach is adopted to transform the problem to a mixed integer quadratically constrained quadratic programming (MI-QCQP) problem. Then, an optimal and a suboptimal algorithm are proposed based on the branch and bound (BnB) method. In addition, a heuristic algorithm is designed in order to trade off the performance between computational complexity and accuracy. Simulation results are provided to demonstrate the performance of the proposed algorithms in terms of the number of admitted users and energy consumption.
Exploring the relationship between eating disorder symptoms and substance use severity in women with comorbid PTSD and substance use disorders

Abstract Background: Eating disorders (ED) and substance use disorders (SUD) commonly co-occur, especially in conjunction with posttraumatic stress disorder (PTSD), yet little is known about ED and ED symptoms in women presenting to addiction treatment programs. Objective: We examined the association between ED symptoms and substance use frequency and severity in a sample of women with a DSM IV diagnosis of current SUD and PTSD enrolled in SUD treatment. Method: Participants were 122 women from four substance abuse treatment sites who participated in a multi-site clinical trial through the National Institute of Drug Abuse Clinical Trials Network (NIDA CTN). The Eating Disorder Examination-Questionnaire (EDE-Q), the Clinician’s Administered PTSD Scale (CAPS) and the Addiction Severity Index (ASI) were administered at baseline and correlational analyses were performed. Variables that significantly correlated with EDE-Q total and subscale scores were entered into a linear regression analysis. Results: Scores on the EDE-Q Global scale, as well as the Eating Concern, Weight Concern and Shape Concern subscales of the EDE-Q were significantly associated with Caucasian race/ethnicity, past 30 day opiate use, higher ASI Psychiatric Subscale score and lower ASI Employment Subscale score. Conclusion: Although exploratory, these findings suggest that there may be a relationship between addiction severity, use of certain drugs of abuse and eating disorder symptoms, particularly those involving weight and shape concerns in women with comorbid PTSD and SUD.
Prodromal Signs and Clinical Factors Influencing Outcome in Patients with Intraventricular Rupture of Purulent Brain Abscess

OBJECTIVETo elucidate prodromal signs and clinical factors influencing the prognosis in patients with intraventricular rupture of brain abscess (IVROBA) to prevent and manage this catastrophic condition. METHODSIn this study, 33 consecutive patients with IVROBA diagnosed by computed tomography (CT) were treated. Basic and therapeutic parameters were evaluated as independent predictive factors of a poor prognosis by using univariate analysis. The factors were statistically analyzed based on the interval between initial symptoms and IVROBA. RESULTSPatients with a good outcome were younger (<21 yr old) (P < 0.003) and had fewer complications after IVROBA (P < 0.03). For the most part, these patients had undergone aspiration for brain abscess with ventricular drainage combined with the immediate administration of appropriate intravenous and intrathecal antibiotics (P < 0.02). In just a short time, abscesses located in the parieto-occipital region ruptured into the ventricle (P < 0.004), and those with nonsterile cultures (P < 0.01) developed into IVROBA. Just before IVROBA, patients had severe headaches, signs of meningeal irritation, and a rapidly deteriorating clinical condition within 10 days after the signs of meningeal irritation developed. A CT scan obtained before IVROBA ascertained localized enhancement of the ventricular wall adjacent to the abscess. CONCLUSIONOur findings suggest that signs of meningeal irritation and localized enhancement of the ventricular wall adjacent to the abscess, as observed on CT scans, preceded IVROBA. To decrease the mortality rate associated with purulent brain abscesses, signs forewarning of IVROBA should be recognized, and aggressive management of IVROBA should be initiated. Aggressive CT-guided aspiration of deep-seated abscesses, particularly in the parieto-occipital region, at the time forewarning signs of IVROBA are observed lead to the prevention of IVROBA and an improvement in outcome.
Endoplasmic reticulum reorganizations and Ca2+ signaling in maturing and fertilized oocytes of marine protostome worms: the roles of MAPKs and MPF

Before a proper Ca2+ response is produced at fertilization, oocytes typically undergo a maturation process during which their endoplasmic reticulum (ER) is restructured. In marine protostome worms belonging to the phylum Nemertea, the ER of maturing oocytes forms numerous distinct clusters that are about 5 μm in diameter. After fertilization, mature oocytes with such aggregates generate a normal series of Ca2+ oscillations and eventually disassemble their ER clusters at around the time that the oscillations cease. Immature oocytes, however, lack prominent ER clusters and fail to exhibit repetitive Ca2+ oscillations upon insemination, collectively suggesting that cell cycle-related changes in ER structure may play a role in Ca2+ signaling. To assess the effects of meiotic regulators on the morphology of the ER and the type of Ca2+ response that is produced at fertilization, nemertean oocytes were treated with pharmacological modulators of mitogen-activated protein kinases (MAPKs) or maturation-promoting factor (MPF) prior to confocal microscopic analyses. Based on such imaging studies and correlative assays of kinase activities, MAPKs of the ERK1/2 type (extracellular signal regulated kinases 1/2) do not seem to be essential for either structural reorganizations of the ER or repetitive Ca2+ signaling at fertilization. Conversely, MPF levels appear to modulate both ER structure and the capacity to produce normal Ca2+ oscillations. The significance of these findings is discussed with respect to other reports on ER structure, MPF cycling and Ca2+ signaling in oocytes of deuterostome animals.
Do patients know they are on pain medication agreements? Results from a sample of high-risk patients on chronic opioid therapy.

OBJECTIVE Pain medicine agreements are frequently recommended for use with high-risk patients on chronic opioid therapy. We assessed how consistently pain medicine agreements were used and whether patients were aware that they had signed a pain medicine agreement in a sample of HIV-infected adults prescribed chronic opioid treatment. DESIGN We recruited patients from a longitudinal cohort of community-based HIV-infected adults and recruited the patients' primary care providers (PCPs). The patients completed in-person interviews and PCPs completed mail-based questionnaires about the patients' use of pain medicine agreements. Among patients prescribed chronic opioid therapy, we analyzed the prevalence of pain medicine agreement use, patient factors associated with their use, and agreement between patient and clinician reports of pain agreements. RESULTS We had 84 patient-clinician dyads, representing 38 PCPs. A total of 72.8% of patients fit the diagnostic criteria for a lifetime substance use disorder. PCPs reported using pain medicine agreements with 42.9% of patients. Patients with pain medicine agreements were more likely to be smokers (91.7% vs 58.3%; P = 0.001) and had higher mean scores on the Screener and Opioid Assessment for Patients with Pain (µ = 26.0 [standard deviation, SD] = 9.7) vs µ = 19.5 [SD = 9.3]; P = 0.003). Patients reported having a pain medicine agreement with a sensitivity of 61.1% and a specificity of 64.6%. CONCLUSIONS In a high-risk sample, clinicians were using agreements at a low rate, but were more likely to use them with patients at highest risk of misuse. Patients exhibited low awareness of whether they signed a pain medicine agreement.
Ground Segmentation Based on Loopy Belief Propagation for Sparse 3D Point Clouds

Ground segmentation is an important pre-processing task for local environment perception using 3D LIDAR, and it is particularly challenging in unstructured environments with rough or sloped terrain. To solve the ground segmentation problem we propose a novel cost-based ground measurement model that is incorporated into a Markov Random Field and solved using loopy belief propagation. Our cost-based measurements operate on columns of a cylindrically-binned map of the LIDAR points and provide robust, non-parametric estimates for ground height. These estimates can model ambiguous situations as well as occlusions from nearer objects. A multi-label Markov Random Field in polar coordinates incorporates local smoothness and slope assumptions to filter out obstacles, while at the same time allowing sharp discontinuities in ground height when waranted by the measurements. An efficient loopy belief propagation method is used to solve for the maximum belief ground height at each cell. Experimental results show good performance in rough terrain, particularly in comparison to other local ground segmentation methods.
Essay in econometrics

Das erste Kapitel befasst sich mit dem Thema, dass in dynamischen Paneldaten-Modellen, wo es keine Querschnitts-Abhaengigkeit gibt, die overidentifying Teststatistik das Produkt aus der Anzahl der Querschnitte und des GMM minimand sein sollte. Auf die unbekannten Autokorrelation-Strukturen der Moment-Bedingungen eingehend, werden die Heteroskedastizitaet und der Autokorrelations-konsistente (HAC) Kovarianzmatrix GMM Schaetzer aufgenommen, und es wird gezeigt, dass die Bootstrap Angleichung die Naeherung erster Ordnung uebertrifft. Wie von Kapetanios (2008) vorgeschlagen, konstruiere ich Bootstrap-Samples durch Resampling der gesamten Querschnittseinheiten mit Austausch anstelle von Block Bootstrap. Monte-Carlo-Simulationen zeigen, dass dieser Bootstrap gute Groesseneigenschaften aufweist, welche den Bootstrap mit Arellano und Bond GMM Schaetzern in allen auf unterschiedlichen Parametern basierenden Faellen uebertrefen. Im zweiten Kapitel wurde basierend auf drei Runden der russischen Longitudinal Monitoring Survey (RLMS) das Auftreten von Nichtzahlungen fuer Haushaltsartikel in Russland anhand einer Reihe von Variablen analysiert. Unter Beruecksichtigung des Einflusses des vergangenen Zahlungsverhaltens, zeigte ein durch GMM Methoden geschaetztes dynamisches binaeres Auswahl-Panel-Daten-Modell, dass die Kategorien der Haushalte, die eine hoehere Wahrscheinlichkeit von Nichtzahlungen aufweisen, diejenigen mit Aufzeichnungen von Nichtzahlungen in der Vergangenheit, einem hoeheren Anteil von Versorgungsausgaben, einem arbeitslosen Haushaltsvorstand, mit Kindern im Schulalter sowie Bewohner von nicht privatisierten Wohnungen oder Haeusern sind. Darueber hinaus erscheinen Lohnrueckstaende und Ausmass der Armut eines Haushalts signifikante Faktoren fuer das Auftreten von Zahlungsrueckstanden bei Versorgungsausgaben zu sein. Die Schaetzung legt nahe, dass die Existenz von Nichtzahlungen fuer Versorgungsausgaben sowohl eine Frage der Armut als auch der niedrigen Bereitschaft ist, h\"ohere Rechnungen f\"ur Dienstleistungen des Sektors, dessen umfangreiche Subventionierung nach dem Zusammenbruch der Sowjetunion gestoppt wurde, zu zahlen. Das letzte Kapitel testet die Hypothese der Segmentierung der Arbeitsmaerkte, das heisst, ob formell angestellte Arbeitnehmer deutlich mehr als informell Beschaeftigte verdienen, basierend auf Daten aus der China Health and Nutrition Survey (CHNS). Anstelle eines parametrischen Ansatzes, welcher unter einer Reihe oekonometrischer Probleme leidet, wird der Propensity-Score-Matching-Ansatz fuer die Schaetzung des Lohnvorteils einer formellen Beschaeftigung angewendet. Aus dem Vergleich von Beschaeftigten mit aehnlichen persoenlichen- und Firmen-Eigenschaften kann nicht die Schlussfolgerung gezogen werden, dass formell Angestellte den informell Beschaeftigten hinsichtlich der Einkommenshoehe ueberlegen sind. Ausserdem testen wir die Robustheit unserer Ergebnisse fuer verschiedene Modell-Spezifikationen und die Sensibilitaet fuer unbeobachtete Kovarianten.
Idiopathic nonspecific interstitial pneumonia: report of an American Thoracic Society project.

RATIONALE The 2002 American Thoracic Society/European Respiratory Society classification of idiopathic interstitial pneumonias identified nonspecific interstitial pneumonia (NSIP) as a provisional diagnosis. Concern was expressed that NSIP was a "wastebasket" category, difficult to distinguish from other idiopathic interstitial pneumonias. OBJECTIVES The following questions were addressed: (1) Is idiopathic NSIP a distinct entity? 2) If so, what are its clinical, radiologic and pathologic characteristics? (3) What is the role of radiology and pathology in establishing the diagnosis? (4) To make a diagnosis of idiopathic NSIP, what other disorders need to be excluded and how should this be done? METHODS Investigators who had previously reported cases of idiopathic NSIP were invited to submit cases for review (n = 305). After initial review, cases with complete clinical, radiologic, and pathologic information (n = 193) were reviewed in a series of workshops. MEASUREMENTS AND MAIN RESULTS Sixty-seven cases were identified as NSIP. Mean age was 52 years, 67% were women, 69% were never-smokers, and 46% were from Asian countries. The most common symptoms were dyspnea (96%) and cough (87%); 69% had restriction. By high-resolution computed tomography, the lower lung zones were predominantly involved in 92% of cases; 46% had a peripheral distribution; 47% were diffuse. Most showed a reticular pattern (87%) with traction bronchiectasis (82%) and volume loss (77%). Lung biopsies showed uniform thickening of alveolar walls with a spectrum of cellular to fibrosing patterns. Five-year survival was 82.3%. CONCLUSIONS Idiopathic NSIP is a distinct clinical entity that occurs mostly in middle-aged women who are never-smokers. The prognosis of NSIP is very good.
A multicenter evaluation of the A&D TM-2420 ambulatory blood pressure recorder.

The A&D TM-2420 (A&D Engineering, Milpitas, CA) is an automatic, portable, noninvasive blood pressure (BP) recorder which uses a dual microphone system for the detection of Korotkoff sounds. Its accuracy and clinical performance were assessed in a multicenter study that also addressed issues such as observer agreement and the effects of age, arm circumference, heart rate, posture, and blood pressure level on the observer-device differences. We compared 906 simultaneous, same-arm BP measurements in 151 subjects using the TM-2420 versus two skilled clinicians per site using a teaching stethoscope. The agreement between the TM-2420 and mercury column determinations were within 10 mm Hg for 86 to 91% of systolic readings and 91 to 94% of diastolic readings, depending on the posture; a level of agreement which would receive a 'B+' grade from the recent British Hypertension Society guidelines. The limits of agreement (2 standard deviations about the mean difference) for systolic BP between observers and the TM-2420 tended to be greater for the standing position (-20 to 15 mm Hg) compared to supine (-14 to 12 mm Hg) and seated (-13 to 8 mm Hg) positions. Limits of agreement between the observers and device were not dependent upon age, heart rate, arm size, or blood pressure level. Twenty-four-hour blood pressure monitoring in two of the four centers demonstrated an error code rate of 3.4%, excluding 'retries' that are one of the device's features. These data demonstrate an acceptable level of accuracy and performance of the sixth generation of the TM-2420 for use in clinical practice and research. (ABSTRACT TRUNCATED AT 250 WORDS)
Quality control on mononuclear cells collected for extracorporeal photochemotherapy: comparison between two UV‐A irradiation devices

Recently, MacoPharma released a new UV‐A cell irradiator device (Macogenic G2) for extracorporeal photopheresis (ECP), smaller and lighter than the Macogenic G1 but with no integrated cooling system. We compared the two devices at different working temperatures (G1 at standard irradiation temperature – 21°C – and G2 set by purpose at 34°C) in patients affected with chronic graft‐versus‐host disease and chronic lung allograft dysfunction treated by ECP. We demonstrate that both G1 and G2 devices are efficient in inducing the inhibition of lymphocytic proliferation and mononuclear cells apoptosis after 48 h even when G2 is set at higher‐than‐standard temperature.
Phospholipid synthesis is decreased in neuronal tissue in a mouse model of Sandhoff disease

Sandhoff disease is a progressive neurodegenerative disorder caused by mutations in the HEXB gene which encodes for the β‐subunit of β‐hexosaminidase A and B, resulting in ganglioside GM2 accumulation in the brain. We now demonstrate that phospholipid metabolism is altered in both cultured neurons and in brain tissue from a mouse model of Sandhoff disease, the Hexb–/– mouse. Metabolic labelling using [methyl‐14C]choline and l‐[3‐3H]serine demonstrated reduced incorporation of [methyl‐14C]choline into phospholipids in brain tissue but not in liver or spleen. Phospholipid mass was also reduced in brain. The activities of CTP : phosphocholine cytidylyltransferase (CCT) and phosphatidylserine synthase were also reduced in brain tissue from Hexb–/– mice, probably because of post‐translational modification as no changes were observed in levels of enzyme expression. The relevance of these findings to Sandhoff disease in human patients is strengthened by observations made over 30 years ago on autopsy tissue of Tay Sachs and Sandhoff disease patients, in which reduced phospholipid levels were observed. We suggest that changes in phospholipid metabolism are not simply because of loss of neuronal tissue as a result of degeneration but rather may cause degeneration, and we discuss the possible effects that changes in phospholipid metabolism could play in the neuropathophysiology of Sandhoff disease.
Rational design for variability minimization in bioanalytical method validation: illustration with LC-MS/MS assay method for terbinafine estimation in human plasma.

Terbinafine, a widely used antifungal drug, is a challenging molecule for quantitative bioanalysis due to certain factors contributing assay variability. Despite previous attempts at human plasma determination of terbinafine, exhaustive stability of the drug or an internal standard was lacking. Internal standard stability with negligible variation throughout the analysis is an indicator of a reliable bioanalytical method as the majority of LC-MS/MS assays are based on analyte/IS response ratios for quantitation. A newly developed high-throughput simple LC-MS/MS method is described for human plasma determination of terbinafine using naftifine internal standard and eluting all compounds within 2 min. A solid-phase extraction of terbinafine achieving mean recovery of 84.3% (CV < 4%) without compromising sensitivity (limit of quantitation 5.11 ng/mL) or linearity (5.11-3014.19 ng/mL) is delineated in this paper. A heated nebulizer in positive multiple reaction monitoring mode was employed with transitions m/z 292.2 →141.1 and 288.2 →117.0 for terbinafine and naftifine, respectively, resulting in excellent chromatographic separation on a Hypurity Advance (50 x 4.6 mm, 5 µm) column. The developed method was successfully applied to clinical samples and for the first time demonstrated marked improved extraction efficiency and reliable long-term plasma stability results without any internal standard response variation during the entire course of study.