Miracle-dz/UniFAR-FTUs huggingface dataset:
AIDS Clinical Trials Group Longitudinal Linked Randomized Trials (ALLRT): Rationale, Design, and Baseline Characteristics

Abstract Purpose: ALLRT is a longitudinal cohort study of HIV-infected subjects prospectively randomized into selected clinical trials for antiretroviral (ARV) treatment-naïve and ARV treatment-experienced individuals conducted by the AIDS Clinical Trials Group (ACTG). We describe the rationale, design, and baseline characteristics of the ALLRT cohort and its potential to address important research questions related to ARV therapy. Method: Standardized visits occur every 16 weeks to evaluate long-term clinical, virologic, and immunologic outcomes associated with ARV treatment. Results: A total of 4,371 subjects enrolled in ALLRT from January 2000 through June 2007. Of these, 3,146 (72%) were ARV naïve at parent study entry (18% female, 44% white, 32% black, 21% Hispanic; median age 37 years, CD4 count 218 cells/μL, follow-up 3.6 years; 343 [11%] followed ⩾8 years) and 1,225 (28%) were treatment experienced (13% female, 59% white, 20% black, 17% Hispanic; median age 42 years, CD4 count 325 cells/μL, follow-up 5.7 years). Conclusions: ALLRT provides the opportunity to understand long-term ramifications of therapeutic ARV choices and determine whether these vary by treatment regimen, timing of treatment initiation, or treatment changes over long-term follow-up. Investigations based on uniform data and specimen collection in the context of randomized ARV treatments will be critical to developing more successful long-term therapeutic strategies for HIV treatment.
Esterase Autodisplay: Enzyme Engineering and Whole-Cell Activity Determination in Microplates with pH Sensors

ABSTRACT Among the GDSL family of serine esterases/lipases is a group of bacterial enzymes that posses C-terminal extensions involved in outer membrane anchoring or translocation. ApeE from Salmonella enterica serovar Typhimurium, a member of this group, has been expressed in Escherichia coli and was resistant to protease digestion when the protease was added to whole cells, indicating a periplasmic localization. The five consensus blocks conserved within all GDSL esterases were identified in ApeE by multiple sequence alignment and separated from the C-terminal extension. The DNA sequence spanning the four invariant residues Ser, Gly, Asn, and His, and hence representing the catalytic domains of ApeE, was amplified by PCR and fused in frame to the transport domains of the autodisplay system. The resulting artificial esterase, called EsjA, was overexpressed in the cell envelope of E. coli and was shown to be active by the use of α-naphthyl acetate (α-NA) as a substrate in an in-gel activity stain after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Surface exposure of EsjA was indicated by its accessibility to protease added to whole cells. The esterase activity of whole cells displaying EsjA was determined by a pH agar assay and by the use of microplates with integrated pH-dependent optical sensors. α-NA, α-naphthyl butyrate, and α-naphthyl caproate were used as substrates, and it turned out that the substrate preferences of artificial EsjA were altered in comparison to original ApeE. Our results indicate that autodisplay of esterase in combination with pH sensor microplates can provide a new platform technology for the screening of tailor-made hydrolase activities.
Preliminary Study on Plateletpheresis with the CS-3000 Blood Cell Separator Using a Single Phlebotomy Technique

A coaxial dual flow catheter has been tested for thrombapheresis with a continuous flow blood cell separator in order to render the procedure as comfortable as possible for our donors. Therefore, two groups of five donors underwent a standard plateletpheresis: 3500 ml of blood were withdrawn at a speed of 35-45 ml per minute and were anticoagulated with ACD-A in a 1/9 ratio to whole blood. In the first group one vein puncture was effectuated with the coaxial catheter after local anesthesia. Two 14G catheters were used in the second group. In both groups the platelet yield was studied as well as the half life of 111-Indium-oxinate labeled platelets after autologous transfusion. Although the comfort of the donors was greatly improved, the one needle procedure resulted in a mean platelet yield of 1,28.1011 while the two needle procedure yielded 3,46.1011 platelets. In contrast, the survival of the platelets after autologous transfusion did not differ significantly in the two groups: t 1/2 in group I was 3,94 d, in group II 3,66 d. It is advocated that the poor efficacy of the single needle procedure might be due to recirculation.
Storage temperatures for cold-chain delivery in cell therapy: a study of alginate-encapsulated liver cell spheroids stored at -80°c or -170°c for up to 1 year.

INTRODUCTION A bioartificial liver comprising alginate-encapsulated liver cell spheroids (ELS) could bridge the gap to transplant or spontaneous recovery in acute liver failure, but will be required for emergency use, necessitating cryopreservation. A cryopreservation protocol has been developed, but beyond this, the feasibility of cold-chain storage is considered here. Cryopreservation will be increasingly required for timely delivery of tissue and bioengineered products, and significant, but often, over-looked factors that impact on cost and ease of clinical application are the storage temperature and useful preservation time. Storage in the vapor phase of liquid nitrogen (∼-170°C) is the gold standard, but for safety and economic purposes, storing ELS in electric freezers at -80°C may be preferable. METHODS ELS were cryopreserved using an optimized protocol and stored at either -80°C or at -170°C for up to 1 year. ELS were removed from storage after 1, 2, 3, 6, 9, or 12 months, and recovery was assessed 24 h postwarming. Cell recovery was assessed using viability (fluorescent staining with image analysis), cell number (nuclei count), and functional (hepatospecific protein enzyme-linked immunosorbent assay) assays. RESULTS Viability, the viable cell number, and function of ELS stored at -170°C were maintained at similar values throughout the year. In contrast, ELS stored at -80°C exhibited decreased viability, viable cell numbers, and function by as early as 1 month. Progressive deterioration was subsequently observed. After 12 months of storage at -80°C, viable cell recovery of ELS was ∼15% that of ELS stored at -170°C. CONCLUSIONS While convenience and cost might support the use of -80°C for storage of multicellular bioengineered products such as ELS, results indicate rapid deterioration in functional recoveries after only a few weeks. This study demonstrates that storage temperature is an important consideration in regenerative medicine and caution should be applied by limiting storage at -80°C to only a few weeks.
Sensitivity enhancement of a QCM biosensor using polymer treatment

Quartz crystal microbalances (QCMs) have been widely used for detection of various chemical and biological species in liquid media. We report an improved binding of protein A and IgG molecules on QCM biosensors by modifying the gold surface of the quartz crystal with a 35 nm polystyrene film followed by an acidic treatment. An appreciable increase in the frequency shift was observed when the polystyrene film was used as an interfacial layer. Protein A and IgG immobilizations on quartz crystals with the polystyrene film represented a 65% increase and a 40% increase respectively when compared to immobilization done directly onto the crystals. Complementary atomic force microscopy (AFM) studies revealed a significant decrease in the RMS roughness of the substrate from 98.4 nm to 1.75 nm when coated with polystyrene. This increased surface smoothness resulted in higher biomolecular coverage on the surface of the sensor causing higher frequency shifts.
3-Benzoyl-4-hydroxy-2-methyl-2H-1,2-benzothiazine 1,1-dioxide

In the title molecule, C16H13NO4S, the heterocyclic thiazine ring adopts a half-chair conformation with the S and N atoms displaced by 0.410 (3) and 0.299 (3) Å, respectively, on opposite sides of the mean plane formed by the remaining ring atoms. The crystal structure is stabilized by intermolecular hydrogen bonds of the types O—H⋯O and C—H⋯O; the former result in dimers lying about inversion centers and the latter form chains of molecules running along the c axis. In addition, intramolecular O—H⋯O links are present.
Significance of Atypical Squamous Cells of Undetermined Significance on ThinPrep Papanicolaou Smears.

Abstract Objective. The aim of this study was to assess the incidence and risk factors predictive of significant histopathologic findings among women with atypical glandular cells of undetermined significance (AGCUS) on ThinPrep Papanicolaou smears. Methods. ThinPrep smears with AGCUS obtained between 1997 and 1999 were reviewed. Patients' charts were reviewed and patients' characteristics, follow-up information, and colposcopy and biopsy results were recorded. Pathologic slides were reviewed. The demographic features of women with favor reactive smears were compared with those with favor neoplasia and risk factors predictive of significant histopathologic findings (high-grade squamous intraepithelial lesion, endometrial hyperplasia, and cervical or endometrial cancers) were calculated. Results. The rate of diagnosis of AGCUS was 0.65%. Eighty-four patients with follow-up information were identified. The demographic features of women with smears favor neoplasia ( n = 43) were similar to those with smears favor reactive ( n = 41). The rates of incidence of any dysplasia or cancer and significant histopathologic findings were 32.1 and 22.6%, respectively, and were higher among women with smears favor neoplasia than among women with smears favor reactive (41.9% versus 22.0%, P = 0.051, and 34.9% versus 9.8%, P = 0.006, respectively). The subtype of cytology was the only factor that predicted significant histopathologic findings (odds ratio=5.0, 95% confidence interval 1.6, 15.6, P Conclusions. In women with AGCUS on ThinPrep smears, significant histopathologic findings were found in 34.9% versus 9.8%, depending on the subtype of the smear (favor neoplasia vs reactive). Further studies are needed to validate the cytologic criteria for subtyping AGCUS smears and base management of women with AGCUS cytology on the subtype of the smear.
CT Analysis of Hindfoot Alignment in Chronic Lateral Ankle Instability

A prospective case-control study was performed comparing axial and coronal CT scan images of 11 patients (14 ankles) with chronic lateral instability and 12 controls. Scans were performed in a standardized fashion to simulate weight-bearing. Nine measurements to evaluate the alignment of the hindfoot and forefoot were made on two occasions by two observers. The blinded images were read in order of assigned random number. The angle between the calcaneus and the vertical plane showed a statistically significant difference between patients (6.4 +/- 4° varus from vertical) and controls (2.7 +/- 5°) using unpaired ANOVA (p < 0.01). Intra-observer (R2 = 0.49 +/-0.19) and interobserver (R2 = 0. 71 +/- 0.13) variation showed moderate reliability across all measurements. This study demonstrates a method to evaluate hindfoot varus on CT scan. Many factors have been studied (e.g., proprioception) as the cause for recurrent instability, and this is the first time, to our knowledge, that an anatomic cause has been demonstrated. Although calcaneal osteotomy is clearly not indicated routinely, it may have a role in correcting extreme varus, which may contribute to failed ligament reconstruction in patients with ankle instability.
How Does Intrinsic Motivation Improve Auditor Judgment in Complex Audit Tasks?

Despite a lack of evidence and theory about specific mechanisms, intrinsic motivation is generally thought to be associated with increased performance on a variety of tasks. We develop theory in this important area and test whether prompting auditors’ intrinsic motivation can solve a critical problem in financial reporting — insufficient auditor skepticism about management estimates. We find that prompting auditors’ intrinsic motivation enhances skepticism by improving auditors’ information processing strategies: prompted auditors attend to a broader set of information, process information at a deeper level, and request more relevant additional evidence. Supplemental analyses show that prompted auditors improve decision effectiveness without sacrificing efficiency and that auditors’ improved skepticism comes mainly from their use of information cues that require higher levels of processing. In sum, we find that prompting auditors’ intrinsic motivation causes auditors to engage in complex cognition that facilitates improved skepticism and improved financial reports.
Gradientenbasierte stochastische modellprädiktive Regelung unter Verwendung der Unscented-Transformation

Zusammenfassung Der Beitrag stellt ein Verfahren zur stochastischen modellprädiktiven Regelung nichtlinearer Systeme vor, wobei das unsichere Systemverhalten durch eine stochastische Differentialgleichung beschrieben wird. Die Unscented-Transformation wird eingesetzt, um die Evolution der Wahrscheinlichkeitsverteilung durch eine Prädiktion von Mittelwert und Kovarianz zu ersetzen. Das resultierende deterministische Problem kann effizient numerisch mit einem Gradientenverfahren gelöst werden.
The Veterans Aging Cohort Study Index is Associated With Concurrent Risk for Neurocognitive Impairment

Objective:The Veterans Aging Cohort Study (VACS) Index is predictive of mortality and combines age, traditional HIV biomarkers (HIV-1 plasma RNA and current CD4 count), and non-HIV biomarkers (indicators of renal and liver function, anemia, and hepatitis C coinfection). We examined the association between the VACS Index and HIV-associated neurocognitive impairment (NCI). Design and Methods:Participants included 601 HIV-infected adults enrolled in cohort studies at the University of California, San Diego, HIV Neurobehavioral Research Program (ages: 18–76 years; 88% male; 63% white; median current CD4 = 364 cells/mm3; 63% on antiretroviral therapy; AIDS = 64%). Biomarkers used in calculating the VACS Index were measured in prospectively collected blood samples using conventional laboratory methods. NCI was defined using global and seven domain deficit scores. Results:Higher VACS Index scores were associated with concurrent risk for global NCI [P < 0.001; odds ratio = 1.21, confidence interval (CI): 1.12 to 1.32], even when adjusting for psychiatric comorbidities. This relation was statistically significant for most cognitive domains in adjusted models. Furthermore, the VACS Index predicted concurrent NCI beyond nadir CD4 and estimated duration of infection. Older age, lower hemoglobin, and lower CD4 counts were the VACS components most strongly linked to NCI. Conclusions:The findings extend previous research on the potential usefulness of the VACS Index in predicting HIV-associated outcomes to include NCI. Although the effect size was relatively small, our findings suggest that demographic information, HIV-disease factors, and common comorbidities might each play important roles in the clinical manifestation of cognitive impairment among HIV-infected individuals. Additional research is needed to determine if a more sensitive and specific index can be developed.
Hashing in the zero shot framework

This paper provides a framework to hash images containing instances of unknown object classes. In many object recognition problems, we might have access to huge amount of data. It may so happen that even this huge data do not cover the objects belonging to classes that we see in our day to day life. Zero shot learning exploits auxiliary information (also called as signatures) in order to predict the labels corresponding to unknown classes. In this work, we attempt to generate the hash codes for images belonging to unseen classes, information of which is available only through the textual corpus. We formulate this as an unsupervised hashing formulation as the exact labels are not available for the instances of unseen classes. We show that the proposed solution is able to generate hash codes which can predict labels corresponding to unseen classes with appreciably good precision.
Spatiotemporal Pattern of Neural Processing in the Human Auditory Cortex

The principles that the auditory cortex uses to decipher a stream of acoustic information have remained elusive. Neural responses in the animal auditory cortex can be broadly classified into transient and sustained activity. We examined the existence of similar principles in the human brain. Sound-evoked, blood oxygen level–dependent signal response was decomposed temporally into independent transient and sustained constituents, which predominated in different portions—core and belt—of the auditory cortex. Converging with unit recordings, our data suggest that this spatiotemporal pattern in the auditory cortex may represent a fundamental principle of analyzing sound information.
A Rorschach analysis: parallel disturbance in thought and in self/object representation.

The relationship between thought process disturbance and the structure of internal object relations was investigated by comparing Rorschach Special Scorings and content variables that reflected developmental levels of object relations. Selected Special Scorings from the Comprehensive System (Exner, 1990) and composite (WSum6) scores were correlated with Urist's (1977) Mutuality of Autonomy Scale (MOA) on the Rorschach protocols of 35 borderlines, 15 schizophrenics, and 19 narcissists. Correlations between composite scores of severe thought process disturbance and severe imbalance in internalized object representations were highly significant, p < . 0001. The hypothesis that there is a significant relationship between disturbance in internalized self/object differentiation and thought process disturbance was supported. Implications of this study are discussed as they relate to empirical validation of theoretical constructs concerning ego function deficit and self/object disturbance.
Structural proportional hazards models for the effects of observed exposures based on interval censored survival data in randomized clinical trials

We target estimating causal effects on the time to an event of interest, which is subject to interval censoring in randomized placebo-controlled clinical trials. Different subjects were observed to receive different doses of treatment which in turn may depend on unmeasured prognostic factors. Consistent estimators for the causal effect of selective treatment exposures exist but allow for right censored failure time data only. We formalize the causal effect in a structural proportional hazards (SPH) model (Loeys and Goetghebeur, 2002). In addition a model is imposed for the association between treatment exposure and treatment-free survival probability. The partial likelihood score (PLS) ∗Correspondence to: An Vandebosch, Dept of Applied Mathematics and Computer Science, Ghent University. Krijgslaan 281, S9; B-9000 Ghent; Belgium. Tel +32-(0)9-264 47 56. Fax +32-(0)9-264 49 95. Email: An.Vandebosch@UGent.be
Road Traffic Correlations with Economic Variables : The Big Data Perspective

Road traffic demand is an interesting topic of research for a wide variety of policymakers. Traffic elasticity, which shows the responsiveness of traffic intensity to other variables, can predict future demand. Existing research on this topic mainly uses survey and panel data. This paper uses big data from the National Database of Road Traffic in the Netherlands to study the correlation between road traffic intensity in different vehicle categories and several economic variables. The purpose of this paper is to extend earlier research results by using a new, different and very comprehensive data source compared to earlier studies. This study shows that there exist correlations between road traffic intensity and multiple economic variables. Most notable are the correlations between total traffic intensity and income (0.74), small vehicle traffic intensity and income (0.74) and the correlation between large vehicle traffic intensity and GDP (0.70). It also concludes that the road traffic in the Netherlands is increasing during the research period of four recent years.
Detection of infection in loosened hip prostheses: efficacy of sonography.

OBJECTIVE The purpose of this study was to determine the efficacy of sonography in the detection of infection in loosened hip prostheses. MATERIALS AND METHODS The normal capsular morphology in 15 asymptomatic patients with total hip replacements was studied sonographically. Sonograms were then obtained in 33 patients who had pain in the hip after arthroplasty and radiologic findings of loosening of the prosthesis. These patients subsequently underwent aspiration and arthrography of the hip. Six of the 33 symptomatic patients proved to have prosthetic joint infection. RESULTS On sonograms, the normal pseudocapsule is adherent to the proximal part of the anterior femoral cortex, and the capsule-to-bone distance is less than 3.2 mm (average, 2.6 mm). No hips with a capsule-to-bone distance less than 3.2 mm were infected. Sonograms in the six patients with infection showed marked intraarticular effusion with a mean capsule-to-bone distance of 10.2 mm. Five of these six had extracapsular fluid collections. Two patients with hip dislocations and four with aseptic loosening of the prosthesis had capsular distension on sonograms and cultures of aspirated material that showed no growth. CONCLUSION Sonography can be used to diagnose infection around loosened hip prostheses. All patients who had an intraarticular effusion with extraarticular extension seen on sonograms had infection.
Microbial population dynamics and diversity during a bloom of the marine coccolithophorid Emiliania huxleyi (Haptophyta)

Several previous studies have shown that Emiliania huxleyi blooms and terminations have been succeeded by an increase in large virus-like particles (LVLP), strongly suggesting the bloom collapse was caused by viral lysis. However, due to methodological limitations, knowledge of how such blooms affect the rest of the microbial community is limited. In the current study we induced a bloom of E. huxleyi in seawater enclosures and applied methods enabling us to describe the algae, bacteria and virus communities with greater resolution than has been done previously. The development of the dominating algal, viral and bacterial populations in the nutrient-amended sea- water enclosures was followed by flow cytometry (FCM). Light microscopy (LM), PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and pulsed-field gel electrophoresis (PFGE) were used to describe the changes in community composition in greater detail. The algal community was domi- nated by E. huxleyi until termination of the bloom by viral lysis. After bloom termination the addi- tional algal populations present in the enclosures increased in abundance. A marked increase in viruses other than the one infecting E. huxleyi was also observed. Total bacterial number and com- munity composition were also greatly influenced by the bloom and its collapse.
Direct Democracy for Transition Countries

Theoretical arguments and empirical evidence are advanced to bolster the claim that direct political participation via referenda and initiatives constitutes an advanced form of democracy with beneficial effects on Transition Countries.nDirect democracy raises trust and honesty and improves social outcomes. Per capita incomes and subjective well-being are raised.nStandard arguments against direct democracy (citizens' incompetence and lacking interest, danger of manipulation and emotionality, hindering progress and destroying civil rights, high cost) are rejected.nElements of direct democracy can be introduced at the national and local levels, and then proceeding further. Citizens should have the right to govern this process.n