Miracle-dz/UniFAR-FTUs huggingface dataset:
Reasons for Ineligibility in Phase 1 and 2A HIV Vaccine Clinical Trials at Kenya Aids Vaccine Initiative (KAVI), Kenya

Background With the persistent challenges towards controlling the HIV epidemic, there is an ongoing need for research into HIV vaccines and drugs. Sub-Saharan African countries - worst affected by the HIV pandemic - have participated in the conduct of clinical trials for HIV vaccines. In Kenya, the Kenya AIDS Vaccine Initiative (KAVI) at the University of Nairobi has conducted HIV vaccine clinical trials since 2001. Methodology Participants were recruited after an extensive informed consent process followed by screening to determine eligibility. Screening included an assessment of risk behavior, medical history and physical examination, and if clinically healthy, laboratory testing. In the absence of locally derived laboratory reference ranges, the ranges used in these trials were derived from populations in the West. Principal findings Two hundred eighty-one participants were screened between 2003 and 2006 for two clinical trials. Of these, 167 (59.4%) met the inclusion/exclusion criteria. Overall, laboratory abnormalities based on the non-indigenous laboratory references used were the most frequent reasons (61.4%) for ineligibility. Medical abnormalities contributed 30.7% of the total reasons for ineligibility. Based on the laboratory reference intervals now developed from East and Southern Africa, those ineligible due to laboratory abnormalities would have been 46.3%. Of the eligible participants, 18.6% declined enrolment. Conclusions Participant recruitment for HIV vaccine clinical trials is a rigorous and time-consuming exercise. Over 61% of the screening exclusions in clinically healthy people were due to laboratory abnormalities. It is essential that laboratory reference ranges generated from local populations for laboratory values be used in the conduct of clinical trials to avoid unnecessary exclusion of willing participants and to avoid over-reporting of adverse events for enrolled participants. Trial registration Protocol IAVI VRC V001 [1]. ClinicalTrials.gov NCT00124007 Protocol IAVI 010 [2] (registration with ClincalTrials.gov is in progress) Protocols IAVI 002 and IAVI 004 are Phase 1 trials only mentioned in introductory paragraphs; details will not be reported. Registration was not required when they were conducted.
DenseSLAM: Simultaneous Localization and Dense Mapping

This paper addresses the problem of environment representation for Simultaneous Localization and Mapping (SLAM) algorithms. One of the main problems of SLAM is how to interpret and synthesize the external sensory information into a representation of the environment that can be used by the mobile robot to operate autonomously. Traditionally, SLAM algorithms have relied on sparse environment representations. However, for autonomous navigation, a more detailed representation of the environment is necessary, and the classic feature-based representation fails to provide a robot with sufficient information. While a dense representation is desirable, it has not been possible for SLAM paradigms. This paper presents DenseSLAM, an algorithm to obtain and maintain detailed environment representations. The algorithm represents different sensory information in dense multi-layered maps. Each layer can represent different properties of the environment, such as occupancy, traversability, elevation or each layer can describe the same environment property using different representations. Implementations of the algorithm with two different representations for the dense maps are shown. A rich representation has several potential advantages to assist the navigation process, for example to facilitate data association using multi-dimensional maps. This paper presents two particular applications to improve the localization process; the extraction of complex landmarks from the dense maps and the detection of areas with dynamic objects. The paper also presents an analysis of consistency of the maps obtained with DenseSLAM. The position error in the dense maps is analyzed and a method to select the landmarks in order to minimize these errors is explained. The algorithm was tested with outdoor experimental data taken with a ground vehicle. The experimental results show that the algorithm can obtain dense environment representations and that the detailed representation can be used to improve the vehicle localization process.
A pilot study of oral calcitriol (1,25-dihydroxyvitamin D3) for relapsing–remitting multiple sclerosis

Background: Epidemiological and ecological studies suggest links between vitamin D deficiency and increased multiple sclerosis (MS) prevalence. Objective: To evaluate the safety and tolerability of oral calcitriol therapy in an open label pilot study. Methods: 15 ambulatory patients with relapsing–remitting MS and at least one clinical relapse within the previous 12 months received oral calcitriol (target dose: 2.5 μg/d) for 48 weeks. Dietary calcium was restricted to 800 mg/d. Patients were monitored using frequent clinical and laboratory examinations, the expanded disability status scale (EDSS), and brain magnetic resonance imaging (MRI). Results: Two patients withdrew because of symptomatic hypercalcaemia (serum calcium >3.35 mmol/l in each case) resulting from persistent dietary indiscretion. Two diet compliant patients required temporary dose adjustments for mild asymptomatic hypercalcaemia. Diet compliant patients experienced mild adverse effects. The on-study exacerbation rate (27%) was less than baseline. Four patients experienced five clinical relapses but only one patient worsened by >1 EDSS point. Brain MRI revealed enhancing lesions in five patients at baseline (33%) and in four (29%) at both 24 and 48 weeks. Conclusions: Oral calcitriol is safe and well tolerated for up to one year by diet compliant relapsing–remitting MS patients. Further study of vitamin D related mechanisms is warranted in MS.
'Sleepwalking to segregation'?: Challenging myths about race and migration

Introduction Making sense of race statistics Challenging the myth that "Britain takes too many immigrants" Challenging the myth that "so many minorities can't be integrated" Challenging the myth that "minorities don't want to integrate" Challenging the myth that "Britain is becoming a country of ghettos" Challenging the myth of "minority white cities" Conclusion Myths and counterarguments: a quick reference summary.
Structural and Molecular Mechanisms of Gap Junction Remodeling in Epicardial Border Zone Myocytes following Myocardial Infarction

Lateralization of the ventricular gap junction protein connexin 43 (Cx43) occurs in epicardial border zone myocytes following myocardial infarction (MI) and is arrhythmogenic. Alterations in Cx43 protein partners have been hypothesized to play a role in lateralization although mechanisms by which this occurs are unknown. To examine potential mechanisms we did nuclear magnetic resonance, yeast 2-hybrid, and surface plasmon resonance studies and found that the SH3 domain of the tyrosine kinase c-Src binds to the Cx43 scaffolding protein zonula occludens-1 (ZO-1) with a higher affinity than does Cx43. This suggests c-Src outcompetes Cx43 for binding to ZO-1, thus acting as a chaperone for ZO-1 and causing unhooking from Cx43. To determine whether c-Src/ZO-1 interactions affect Cx43 lateralization within the epicardial border zone, we performed Western blot, immunoprecipitation, and immunolocalization for active c-Src (p-cSrc) post-MI using a canine model of coronary occlusion. We found that post-MI p-cSrc interacts with ZO-1 as Cx43 begins to decrease its interaction with ZO-1 and undergo initial loss of intercalated disk localization. This indicates that the molecular mechanisms by which Cx43 is lost from the intercalated disk following MI includes an interaction of p-cSrc with ZO-1 and subsequent loss of scaffolding of Cx43 leaving Cx43 free to diffuse in myocyte membranes from areas of high Cx43, as at the intercalated disk, to regions of lower Cx43 content, the lateral myocyte membrane. Therefore shifts in Cx43 protein partners may underlie, in part, arrhythmogenesis in the post-MI heart.
Linear universal demosaicking of regular pattern color filter arrays

We show that a recently developed universal demosaicker by the present authors greatly outperforms existing demosaickers when tested with a realistic optical pipeline. We present speed and quality optimizations of this demosaicker for the case of regular pattern color filter arrays. We implement and extensively test optimized versions for several common CFAs including Bayer, CMY and several RGBW patterns. These tests show that the proposed algorithms outperform other demosaickers by a substantial margin while being faster than most of them. High sensitivity RGBW CFAs are shown to have better performance than Bayer demosaicked with previous algorithms. The proposed universal demosaicker is a set of Finite Impulse Response Filters, which allows a single, efficient, Image Signal Processor design to support different CFAs by changing its filter weights. Being linear, the demosaicker is free of noise induced artifacts and outputs images with near Poissonian noise which is noise reduction friendly.
Interval set: a volume rendering technique generalizing isosurface extraction

A scalar volume V={(x,f(x))|x/spl isin/R} is described by a function f(x) defined over some region R of the three dimensional space. The paper presents a simple technique for rendering interval sets of the form I/sub g/(a,b)={(x,f(x))|a/spl les/g(x)/spl les/b}, where a and b are either real numbers of infinities. We describe an algorithm for triangulating interval sets as /spl alpha/ shapes, which can be accurately and efficiently rendered as surfaces or semi transparent clouds. On the theoretical side, interval sets provide an unified approach to isosurface extraction and direct volume rendering. On the practical side, interval sets add flexibility to scalar volume visualization-we may choose to, for example, have an interactive, high quality display of the volume surrounding or "inside" an isosurface when such display for the entire volume is too expensive to produce.
Effects of dietary salt on angiotensin peptides in kidney.

This study used a novel simple method for the extraction, separation, identification, and quantitation of angiotensin-like immunoactivity from tissue to examine the effects of altering dietary NaCl intake on intrarenal angiotensin I, II, and III levels in salt-sensitive, spontaneously hypertensive rats, salt-resistant Wistar-Kyoto rats, and Sprague-Dawley rats. Seven-week-old male spontaneously hypertensive rats, Wistar-Kyoto rats, and Sprague-Dawley rats were assigned randomly to a diet containing either 8% (high) or 1% (basal) salt and were maintained on these diets for 3 wk. Rats were then decapitated without prior anesthesia, and kidneys were rapidly (< 30 s) removed, snap frozen in liquid nitrogen, and stored at -80 degrees C. Frozen tissue was extracted in 2 M acetic acid and then subjected to solid-phase extraction with the cation exchange resin AG 50W X4. Angiotensin peptides were separated by reversed-phase high-performance liquid chromatography on a phenyl silica gel column with an eluent consisting of 20% acetonitrile in 0.1 M ammonium phosphate buffer, pH 4.9, and quantitated by radioimmunoassay. The elution of standard peptides under isocratic conditions revealed clear resolution of angiotensin I, II, and III and the (1-7) and (3-8) peptides. Recoveries of both labeled and unlabeled angiotensin peptide standards from the extraction step were > 90%. Renal angiotensin II stores were significantly higher in spontaneously hypertensive rats than in Wistar-Kyoto or Sprague-Dawley rats, independent of diet. Renal angiotensin II and III were further suppressed during dietary salt supplementation in both salt-resistant strains but not in the spontaneously hypertensive rat. These findings are consistent with an enhanced (compared with Wistar-Kyoto and Sprague-Dawley rats) role for angiotensin II in the kidney of the salt-sensitive, spontaneously hypertensive rat, particularly under conditions of dietary salt supplementation.
Efficiency of Repeated Phytoextraction of Cadmium and Zinc from an Agricultural Soil Contaminated with Sewage Sludge

Long-term application of sewage sludge resulted in soil cadmium (Cd) and zinc (Zn) contamination in a pot experiment conducted to phytoextract Cd/Zn repeatedly using Sedum plumbizincicola and Apium graceolens in monoculture or intercropping mode eight times. Shoot yields and soil physicochemical properties changed markedly with increasing number of remediation crops when the two plant species were intercropped compared with the unplanted control soil and the two monoculture treatments. Changes in soil microbial indices such as average well colour development, soil enzyme activity and soil microbial counts were also significantly affected by the growth of the remediation plants, especially intercropping with S. plumbizincicola and A. graveolens. The higher yields and amounts of Cd taken up indicated that intercropping of the hyperaccumulator and the vegetable species may be suitable for simultaneous agricultural production and soil remediation, with larger crop yields and higher phytoremediation efficiencies than under monoculture conditions.
Noise Reduction of MEMS Gyroscope Based on Direct Modeling for an Angular Rate Signal

In this paper, a novel approach for processing the outputs signal of the microelectromechanical systems (MEMS) gyroscopes was presented to reduce the bias drift and noise. The principle for the noise reduction was presented, and an optimal Kalman filter (KF) was designed by a steady-state filter gain obtained from the analysis of KF observability. In particular, the true angular rate signal was directly modeled to obtain an optimal estimate and make a self-compensation for the gyroscope without needing other sensor’s information, whether in static or dynamic condition. A linear fit equation that describes the relationship between the KF bandwidth and modeling parameter of true angular rate was derived from the analysis of KF frequency response. The test results indicated that the MEMS gyroscope having an ARW noise of 4.87°/h0.5 and a bias instability of 44.41°/h were reduced to 0.4°/h0.5 and 4.13°/h by the KF under a given bandwidth (10 Hz), respectively. The 1σ estimated error was reduced from 1.9°/s to 0.14°/s and 1.7°/s to 0.5°/s in the constant rate test and swing rate test, respectively. It also showed that the filtered angular rate signal could well reflect the dynamic characteristic of the input rate signal in dynamic conditions. The presented algorithm is proved to be effective at improving the measurement precision of the MEMS gyroscope.
Pathwise convergent higher order numerical schemes for random ordinary differential equations

Random ordinary differential equations (RODEs) are ordinary differential equations (ODEs) with a stochastic process in their vector field. They can be analysed pathwise using deterministic calculus, but since the driving stochastic process is usually only Hölder continuous in time, the vector field is not differentiable in the time variable, so traditional numerical schemes for ODEs do not achieve their usual order of convergence when applied to RODEs. Nevertheless deterministic calculus can still be used to derive higher order numerical schemes for RODEs via integral versions of implicit Taylor-like expansions. The theory is developed systematically here and applied to illustrative examples involving Brownian motion and fractional Brownian motion as the driving processes.
Can Digital Pathology Result In Cost Savings? A Financial Projection For Digital Pathology Implementation At A Large Integrated Health Care Organization

Background: Digital pathology offers potential improvements in workflow and interpretive accuracy. Although currently digital pathology is commonly used for research and education, its clinical use has been limited to niche applications such as frozen sections and remote second opinion consultations. This is mainly due to regulatory hurdles, but also to a dearth of data supporting a positive economic cost-benefit. Large scale adoption of digital pathology and the integration of digital slides into the routine anatomic/surgical pathology "slide less" clinical workflow will occur only if digital pathology will offer a quantifiable benefit, which could come in the form of more efficient and/or higher quality care. Aim: As a large academic-based health care organization expecting to adopt digital pathology for primary diagnosis upon its regulatory approval, our institution estimated potential operational cost savings offered by the implementation of an enterprise-wide digital pathology system (DPS). Methods: Projected cost savings were calculated for the first 5 years following implementation of a DPS based on operational data collected from the pathology department. Projected savings were based on two factors: (1) Productivity and lab consolidation savings; and (2) avoided treatment costs due to improvements in the accuracy of cancer diagnoses among nonsubspecialty pathologists. Detailed analyses of incremental treatment costs due to interpretive errors, resulting in either a false positive or false negative diagnosis, was performed for melanoma and breast cancer and extrapolated to 10 other common cancers. Results: When phased in over 5-years, total cost savings based on anticipated improvements in pathology productivity and histology lab consolidation were estimated at $12.4 million for an institution with 219,000 annual accessions. The main contributing factors to these savings were gains in pathologist clinical full-time equivalent capacity impacted by improved pathologist productivity and workload distribution. Expanding the current localized specialty sign-out model to an enterprise-wide shared general/subspecialist sign-out model could potentially reduce costs of incorrect treatment by $5.4 million. These calculations were based on annual over and under treatment costs for breast cancer and melanoma estimated to be approximately $26,000 and $11,000/case, respectively, and extrapolated to $21,500/case for other cancer types. Conclusions: The projected 5-year total cost savings for our large academic-based health care organization upon fully implementing a DPS was approximately $18 million. If the costs of digital pathology acquisition and implementation do not exceed this value, the return on investment becomes attractive to hospital administrators. Furthermore, improved patient outcome enabled by this technology strengthens the argument supporting adoption of an enterprise-wide DPS.
Poor sensitivity of field rapid HIV testing: implications for mother‐to‐child transmission programme

We validated rapid HIV tests among pregnant women in a clinical setting. Field testing was performed using First Response 1,2,3 or Standard Diagnostic and Pareekshak tests. Results were confirmed by third generation HIV ELISA. Discordant or negative, specimens were confirmed by RNA PCR and a fourth generation ELISA test. Sensitivity and specificity were 94.5% (CI: 85.8–98.2) and 100% for First Response; 87.5% (CI: 46.7–99.3) and 100% (CI: 87.7–100%) for Standard Diagnostic and 90.2% (CI: 81.2–95.4) and 100% (CI: 98–100%) for Pareekshak. These sensitivities were lower than laboratory validation which approached 100%. The low‐field sensitivity results have implications for Prevention of Mother‐to‐Child Transmission services.
Office referrals and suspension: Disciplinary intervention in middle schools.

While school discipline and student behavior represent major concerns to the public and to the schools, surprisingly little research has been completed on the disciplinary referrals of students for discipline or inappropriate behavior. This report, consisting of two studies conducted in two Midwestern cities (one across multiple schools, and the other in a single school), examines a variety of descriptive issues related to school discipline as documented in archived office disciplinary referral data. These were analyzed in order to examine the reasons for the referral, circumstances of the situation, the extent of use of various disciplinary response options, the rate of student suspension, and other characteristics of the disciplinary incidents. Behaviors that led to office referral were primarily not those that threaten safety, but those that indicate noncompliance or disrespect. In both studies, about 40% of all students receive at least one office referral in the middle school during the school year. RESULTS indicated that most disciplinary referrals originate in the classroom, and provided little evidence of a consistent relationship between seriousness of offense and severity of consequence. Finally, these studies show a pattern of disproportionality in the administration of school discipline based on race, SES, gender and disability. Language: en
Transcriptional Responses of Arabidopsis thaliana during Wilt Disease Caused by the Soil-Borne Phytopathogenic Bacterium, Ralstonia solanacearum

Bacterial wilt is a common disease that causes severe yield and quality losses in many plants. In the present study, we used the model Ralstonia solanacearum-Arabidopsis thaliana pathosystem to study transcriptional changes associated with wilt disease development. Susceptible Col-5 plants and RRS1-R-containing resistant Nd-1 plants were root-inoculated with R. solanacearum strains harbouring or lacking the matching PopP2 avirulence gene. Gene expression was marginally affected in leaves during the early stages of infection. Major changes in transcript levels took place between 4 and 5 days after pathogen inoculation, at the onset of appearance of wilt symptoms. Up-regulated genes in diseased plants included ABA-, senescence- and basal resistance-associated genes. The influence of the plant genetic background on disease-associated gene expression is weak although some genes appeared to be specifically up-regulated in Nd-1 plants. Inactivation of some disease-associated genes led to alterations in the plant responses to a virulent strain of the pathogen. In contrast to other pathosystems, very little overlap in gene expression was detected between the early phases of the resistance response and the late stages of disease development. This observation may be explained by the fact that above-ground tissues were sampled for profiling whereas the bacteria were applied to root tissues. This exhaustive analysis of Arabidopsis genes whose expression is modulated during bacterial wilt development paves the way for dissecting plant networks activated by recognition of R. solanacearum effectors in susceptible plants.
Mitochondrial energy generation disorders: genes, mechanisms, and clues to pathology

Inherited disorders of oxidative phosphorylation cause the clinically and genetically heterogeneous diseases known as mitochondrial energy generation disorders, or mitochondrial diseases. Over the last three decades, mutations causing these disorders have been identified in almost 290 genes, but many patients still remain without a molecular diagnosis. Moreover, while our knowledge of the genetic causes is continually expanding, our understanding into how these defects lead to cellular dysfunction and organ pathology is still incomplete. Here, we review recent developments in disease gene discovery, functional characterization, and shared pathogenic parameters influencing disease pathology that offer promising avenues toward the development of effective therapies.