Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental study of tuberculosis: From animal models to complex cell systems and organoids

Tuberculosis (TB) is a devastating disease to mankind that has killed more people than any other infectious disease. Despite many efforts and successes from the scientific and health communities, the prospect of TB elimination remains distant. On the one hand, sustainable public health programs with affordable and broad implementation of anti-TB measures are needed. On the other hand, achieving TB elimination requires critical advances in three areas: vaccination, diagnosis, and treatment. It is also well accepted that succeeding in advancing these areas requires a deeper knowledge of host—pathogen interactions during infection, and for that, better experimental models are needed. Here, we review the potential and limitations of different experimental approaches used in TB research, focusing on animal and human-based cell culture models. We highlight the most recent advances in developing in vitro 3D models and introduce the potential of lung organoids as a new tool to study Mycobacterium tuberculosis infection.
Omega-3 Index and Sudden Cardiac Death

Sudden cardiac death (SCD) is an unresolved health issue, and responsible for 15% of all deaths in Western countries. Epidemiologic evidence, as well as evidence from clinical trials, indicates that increasing intake and high levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) protect from SCD and other major adverse cardiac events. Levels of EPA+DHA are best assessed by the Omega-3 Index, representing the red cell fatty acid content of EPA+DHA. Work is in progress that will further define the value of the Omega-3 Index as a risk factor for SCD, other cardiac events, and as target for treatment with EPA+DHA.
Variance‐components methods for linkage and association analysis of ordinal traits in general pedigrees

Many complex human diseases such as alcoholism and cancer are rated on ordinal scales. Well‐developed statistical methods for the genetic mapping of quantitative traits may not be appropriate for ordinal traits. We propose a class of variance‐component models for the joint linkage and association analysis of ordinal traits. The proposed models accommodate arbitrary pedigrees and allow covariates and gene‐environment interactions. We develop efficient likelihood‐based inference procedures under the proposed models. The maximum likelihood estimators are approximately unbiased, normally distributed, and statistically efficient. Extensive simulation studies demonstrate that the proposed methods perform well in practical situations. An application to data from the Collaborative Study on the Genetics of Alcoholism is provided. Genet. Epidemiol. 34: 232–237, 2010. © 2009 Wiley‐Liss, Inc.
Temporal relationship between the development of the self-priming effect of LHRH and changes in serum concentrations of testosterone and androstenedione during the sexual maturation of the male rat.

The pituitaries of pubertal and adult male rats release more LH in response to LHRH if the animals are pretreated with three priming doses of LHRH than if they are pretreated with saline. Immature male rats do not exhibit a similar self-priming response. These studies were designed to determine more precisely the age of onset of this effect and to relate it to the serum levels of androstenedione (A) and testosterone (T). Beginning on Day 30 (immature) and every 4 days thereafter through Day 54 (pubertal), the following experiment was performed. Male rats were anesthetized with ketamine HCI (10-20 mg/kg i.p.) and a 0.7-1.0 ml blood sample was collected by heart puncture for radioimmunoassay of A and T. Next the animals received i.v. injections (tight jugular vein) of 10 ng LHRH/100 g BW or saline at time 0, 30, and 60 mm. At 90 mm an additional blood sample was obtained, and all animals received an i.v. injection of 50 ng LHRH/ 100 g BW via the left jugular. At 100 mm a final blood sample was obtained. LH concentrations in the 90 and 100 mm samples were determined by radioimmunoassay. A statistically significant (P<O.01) self-priming effect was first detected on Day 46. Serum concentrations of T and A were first significantly (P<0.05) elevated and the ratio ALT first significantly (P<0.05) reduced on Day 42. These data suggest that the self-priming effect of LHRH develops in the male rat between Days 42 and 46 and appears to be preceded by alterations in testicular steroid concentrations.
The use of error and uncertainty methods in the medical laboratory

Abstract Error methods – compared with uncertainty methods – offer simpler, more intuitive and practical procedures for calculating measurement uncertainty and conducting quality assurance in laboratory medicine. However, uncertainty methods are preferred in other fields of science as reflected by the guide to the expression of uncertainty in measurement. When laboratory results are used for supporting medical diagnoses, the total uncertainty consists only partially of analytical variation. Biological variation, pre- and postanalytical variation all need to be included. Furthermore, all components of the measuring procedure need to be taken into account. Performance specifications for diagnostic tests should include the diagnostic uncertainty of the entire testing process. Uncertainty methods may be particularly useful for this purpose but have yet to show their strength in laboratory medicine. The purpose of this paper is to elucidate the pros and cons of error and uncertainty methods as groundwork for future consensus on their use in practical performance specifications. Error and uncertainty methods are complementary when evaluating measurement data.
Fast and accurate techniques for measuring the complex transmittance of liquid crystal light valves

A highly accurate measurement technique has been developed and applied for characterization of the complex transmittance of liquid crystal light valves (LC-LV). The measurement setup is based on a two-beam interference with partially coherent light. An arc lamp light source enables measurements over a large range of wavelengths. We propose a new Fourier transform interference pattern evaluation technique with a high signal-to-noise ratio. Calculations are sped up by FFT algorithms. Measurement results of the complex transmittance are shown for a twisted nematic and a Freederickzs liquid crystal light valve, built in our laboratory.
Multicolor Polymer Nanocomposites: In Situ Synthesis and Fabrication of 3D Microstructures

Microstereolithography (MSL) is an emerging technology, which is expected to play a key role in the fabrication of mi- cro-and nanoelectronic machines and micro-and nanoelec-tromechanical systems (MEMS/NEMS). [1] Of the various MSL techniques, multiphoton photopolymerization (MPP) [2–6] has attracted widespread interest owing to its potential use in fabricating intrinsic 3D microstructures such as 3D photonic crystals (PhCs).
Improved Onlooker Bee Phase in Artificial Bee Colony Algorithm

Artificial Bee Colony (ABC) is a distinguished optimization strategy that can resolve nonlinear and multifaceted problems. It is comparatively a straightforward and modern population based probabilistic approach for comprehensive optimization. In the vein of the other population based algorithms, ABC is moreover computationally classy due to its slow nature of search procedure. The solution exploration equation of ABC is extensively influenced by a arbitrary quantity which helps in exploration at the cost of exploitation of the better search space. In the solution exploration equation of ABC due to the outsized step size the chance of skipping the factual solution is high. Therefore, here this paper improve onlooker bee phase with help of a local search strategy inspired by memetic algorithm to balance the diversity and convergence capability of the ABC. The proposed algorithm is named as Improved Onlooker Bee Phase in ABC (IoABC). It is tested over 12 well known un-biased test problems of diverse complexities and two engineering optimization problems; results show that the anticipated algorithm go one better than the basic ABC and its recent deviations in a good number of the experiments.
Baseline Approaches for the Authorship Identification Task - Notebook for PAN at CLEF 2011

In this paper we present the evaluation of three different classifiers (Rocchio, Naive Bayes and Greedy) with the aim of obtaining a baseline in the task of authorship identification. We decided to employ as features the original words contained in each document of the test set, with a minimum of preprocessing which included elimination of stopwords, punctuation symbols and XML tags. As may be seen in this paper, the obtained results are adequate, reflecting the aim of the experiments. In average, Rocchio slightly outperformed the Naive Bayes and the Greedy classifier. However, we recommend using both, Rocchio and Naive Bayes in future evaluations of the PAN competition as baselines from which other teams may compare their own approach.
Short-interval observational data to inform clinical trial design in Huntington's disease

Objectives To evaluate candidate outcomes for disease-modifying trials in Huntington's disease (HD) over 6-month, 9-month and 15-month intervals, across multiple domains. To present guidelines on rapid efficacy readouts for disease-modifying trials. Methods 40 controls and 61 patients with HD, recruited from four EU sites, underwent 3 T MRI and standard clinical and cognitive assessments at baseline, 6 and 15 months. Neuroimaging analysis included global and regional change in macrostructure (atrophy and cortical thinning), and microstructure (diffusion metrics). The main outcome was longitudinal effect size (ES) for each outcome. Such ESs can be used to calculate sample-size requirements for clinical trials for hypothesised treatment efficacies. Results Longitudinal changes in macrostructural neuroimaging measures such as caudate atrophy and ventricular expansion were significantly larger in HD than controls, giving rise to consistently large ES over the 6-month, 9-month and 15-month intervals. Analogous ESs for cortical metrics were smaller with wide CIs. Microstructural (diffusion) neuroimaging metrics ESs were also typically smaller over the shorter intervals, although caudate diffusivity metrics performed strongly over 9 and 15 months. Clinical and cognitive outcomes exhibited small longitudinal ESs, particularly over 6-month and 9-month intervals, with wide CIs, indicating a lack of precision. Conclusions To exploit the potential power of specific neuroimaging measures such as caudate atrophy in disease-modifying trials, we propose their use as (1) initial short-term readouts in early phase/proof-of-concept studies over 6 or 9 months, and (2) secondary end points in efficacy studies over longer periods such as 15 months.
The Influence of Executive Functioning on Facial and Subjective Pain Responses in Older Adults

Cognitive decline is known to reduce reliability of subjective pain reports. Although facial expressions of pain are generally considered to be less affected by this decline, empirical support for this assumption is sparse. The present study therefore examined how cognitive functioning relates to facial expressions of pain and whether cognition acts as a moderator between nociceptive intensity and facial reactivity. Facial and subjective responses of 51 elderly participants to mechanical stimulation at three intensities levels (50 kPa, 200 kPa, and 400 kPa) were assessed. Moreover, participants completed a neuropsychological examination of executive functioning (planning, cognitive inhibition, and working memory), episodic memory, and psychomotor speed. The results showed that executive functioning has a unique relationship with facial reactivity at low pain intensity levels (200 kPa). Moreover, cognitive inhibition (but not other executive functions) moderated the effect of pressure intensity on facial pain expressions, suggesting that the relationship between pressure intensity and facial reactivity was less pronounced in participants with high levels of cognitive inhibition. A similar interaction effect was found for cognitive inhibition and subjective pain report. Consequently, caution is needed when interpreting facial (as well as subjective) pain responses in individuals with a high level of cognitive inhibition.
Validity of Different Linguistic Versions of the Alzheimer’s Disease Assessment Scale in an International Multicentre Alzheimer’s Disease Trial

Owing to the involvement of Italian Centres in a multicentre, German-Italian therapeutical trial with Alzheimer’s dementia patients, to be assessed with the Alzheimer’s Disease Assessment Scale (ADAS), it was decided that the Italian centres would use an Italian version of the scale, derived from that used by the German centres. However, the lists of words for exploring verbal memory are not merely translated from the German version, but are composed of selective Italian words chosen according to linguistic criteria. This Italian version was validated following the same procedure adopted for validating the German version. We submitted this Italian version to an interrater reliability, test-retest reliability, concurrent validity, internal consistency and sensitivity evaluation, using demented patients. Based on the results of these tests this Italian version of the ADAS proved valid and reliable. Moreover, the results were strikingly comparable to those from the validation of the German version. Our work supports the validity, reliability and transnational comparability of national versions of the ADAS constructed following definite linguistic criteria.
Discriminative Power and Retrieval Effectiveness of Phrasal Indexing Terms

In spite of long controversy, effectiveness of phrasal indexing is not yet clear. Recently, correlation between query length and effect of phrasal indexing is reported. In this paper, terms extracted from the topic set of the NACSIS test collection 1 are analyzed utilizing statistic tools in order to show distribution characteristics of single word/phrasal terms with regard to relevant/non-relevant documents. Phrasal terms are found to be very good discriminators in general but not all of them are effective as supplemental phrasal terms. A distinction of informative / neutral / destructive phrasal terms is introduced. Retrieval effectiveness is examined utilizing query weight ratio of these three categories of phrasal terms.
[Establishment and biological characterization of human medulloblastoma cell lines].

Two cell lines of human medulloblastoma (ONS-76 and ONS-81) were established, and their biological characteristics were investigated. The cell line, ONS-76, was established from a tumor specimens obtained from a large cerebellar tumor of a 2-year-old girl. The pathological diagnosis was a typical medulloblastoma. The other cell line, ONS-81, was derived from a metastatic tumor in right frontal lobe of a 9-year-old girl. The tumor specimens were minced into fragments approximately 1 mm in diameter and cultured in plastic culture flasks in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS) and 50% patients serum. The cells growing as a monolayer were subcultured in RPMI 1640 supplemented with 10% FCS and initially with L-glutamine, sodium pyruvate, and nonessential amino acid. Microscopically, both cultured cells exhibited various morphological appearances, and this morphological heterogeneity seemed to be specific for medulloblastoma cells. The in vitro population doubling time of ONS-76 and ONS-81 were 18.6 and 19.2 hr, respectively. The ONS-76 and ONS-81 cells formed subcutaneous tumors in nude mice as serial transplantable xenograft, and these tumors had a microscopic appearance similar to that of the original medulloblastoma. Ultrastructurally++, the cultured cells showed primitive, undifferentiated appearance, and no neuronal or glial structures were not seen. Immunohistochemical studies showed that both cells expressed neuron-specific enolase (NSE) and neurofilament protein (NFP 200 K, 145 K), but glial fibrillary acidic protein (GFAP) and S-100 protein were not detected. The NFP immunoreactivities of both cultured cells were demonstrated as abnormal perinuclear deposits. (ABSTRACT TRUNCATED AT 250 WORDS)
Rosetta: Extracting Protocol Semantics using Binary Analysis with Applications to Protocol Replay and NATRewriting

Rewriting a previously seen dialog between two entities, so that it is accepted by another entity, is important for many applications including: the protocol replay problem and the NAT rewriting problem. Both problems are instances of a larger problem that we call the dialog rewriting problem. The challenge in dialog rewriting is that the dynamic fields, e.g., hostnames, IP addresses, session identifiers or timestamps, in the original dialog need to be rewritten for the modified dialog to succeed. This is particularly difficult because the protocol used in the original dialog might be unknown. In this paper, our goal is to generate a transformation function that can be used to rewrite the values of the dynamic fields. For this, we propose binary analysis techniques to solve the main two challenges: 1) how to automatically identify the dynamic fields, and 2) how to automatically rewrite the values in the dynamic fields. We have implemented Rosetta, a system that creates the transformation function using our proposed techniques. Our results show that we are able to identify different types of dynamic fields present in commonly used protocols such as FTP, DNS and ICQ , and that we are able to rewrite the values in the dynamic fields, even when those fields use complex encodings to represent the data, thus enabling the protocol replay and NAT rewriting problems.
Structural and electronic properties of swift heavy ion tracks in amorphous carbon

Ion irradiation effects in the electronic energy loss regime are discussed for various carbon materials. The formation of tracks in irradiated amorphous carbon is analyzed experimentally in detail using various microscopy techniques (AFM, TEM) and spatially resolved electrical characterization methods. A model is created to simulate the track formation process using classical molecular dynamics.
A novel bradykinin‐like peptide from skin secretions of the frog, Rana nigrovittata

A bradykinin‐like peptide has been isolated from the skin secretions of the frog Rana nigrovittata. This peptide was named ranakinin‐N. Its primary structure, RAEAVPPGFTPFR, was determined by Edman degradation and mass spectrometry. It is structurally related to bradykinin‐like peptides identified from skin secretions of other amphibians. Ranakinin‐N is composed of 13 amino acid residues and is related to the bradykinin identified from the skin secretions of Odorrana schmackeri, which is composed of 9 amino acid residues. Ranakinin‐N was found to exert concentration‐dependent contractile effects on isolated guinea pig ileum. cDNA sequence encoding the precursor of ranakinin‐N was isolated from a skin cDNA library of R. nigrovittata. The amino acid sequences deduced from the cDNA sequences match well with the results from Edman degradation. Analysis of different amphibian bradykinin cDNA structures revealed that the deficiency of a 15‐nucleotide fragment (agaatgatcagacgc in the cDNA encoding bradykinin from O. schmackeri) in the peptide‐coding region resulted in the absence of a dibasic site for trypsin‐like proteinases and an unusual ‐AEVA‐ insertion in the N‐terminal part of ranakinin‐N. The ‐AEAV‐ insertion resulted in neutral net charge at the N‐terminus of ranakinin‐N. Ranakinin‐N is the first reported bradykinin‐like peptide with a neutral net charge at the N‐terminus. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Light Limitation within Southern New Zealand Kelp Forest Communities

Light is the fundamental driver of primary productivity in the marine environment. Reduced light availability has the potential to alter the distribution, community composition, and productivity of key benthic primary producers, potentially reducing habitat and energy provision to coastal food webs. We compared the underwater light environment of macroalgal dominated shallow subtidal rocky reef habitats on a coastline modified by human activities with a coastline of forested catchments. Key metrics describing the availability of photosynthetically active radiation (PAR) were determined over 295 days and were related to macroalgal depth distribution, community composition, and standing biomass patterns, which were recorded seasonally. Light attenuation was more than twice as high in shallow subtidal zones along the modified coast. Macroalgal biomass was 2–5 times greater within forested sites, and even in shallow water (2m) a significant difference in biomass was observed. Long-term light dose provided the best explanation for differences in observed biomass between modified and forested coasts, with light availability over the study period differing by 60 and 90 mol photons m−2 at 2 and 10 metres, respectively. Higher biomass on the forested coast was driven by the presence of larger individuals rather than species diversity or density. This study suggests that commonly used metrics such as species diversity and density are not as sensitive as direct measures of biomass when detecting the effects of light limitation within macroalgal communities.
Programmable Analog-to-Digital Converter for Low-Power DC–DC SMPS

An application-specific delay-line based windowed analog-to-digital converter (ADC) with programmable reference voltage, conversion time, and accuracy of voltage regulation, is introduced. The ADC can be fully implemented on a small silicon area and is suitable for implementation in various integrated digital controllers for high-frequency low-power switch-mode power supplies. The programmable characteristics are achieved through the utilization of the inherent averaging effect of the delay line and through the adjustments of delay cells' propagation times. The ADC is implemented in a standard 0.18 m CMOS technology, as a part of a high-frequency digital controller integrated circuit, and tested with a 1.5 MHz, 1 W buck dc-dc converter.
Diagnostic ability of intraoperative ultrasound for identifying tumor residual in glioma surgery operation

Achieving total glioma resection represents a major challenge to neurosurgeons with no distinct margin between tumor and surrounding brain tissue. Many imaging methods are employed in surgery visualization and resection control. We performed this meta-analysis to assess the diagnosis value of intraoperative ultrasound and judged whether ultrasound is a suitable tool in detecting glioma residual. The databases including PubMed, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), Wanfang and Weipu were systematically searched to find out relevant studies and published up to May 5, 2017. A total of 14 studies involving 542 participants met the selection criteria and bivariate mixed effects models were used for analysis. The parameters and their corresponding 95% confidence interval (CI) were computed on Stata 12.0 software. The pooled sensitivity was 0.75 (95%CI: 0.62–0.84), specificity was 0.88 (95%CI: 0.79–0.94), positive likelihood ratios was 6.27 (95%CI: 3.76–10.47), negative likelihood ratios was 0.29 (95%CI: 0.20–0.42), diagnostic odds ratios was 21.83 (95%CI: 14.20–33.55) and area under the curve of summary receiver operator characteristic was 0.89. Stratified meta-analysis showed sensitivity and area under the curve in low-grade glioma were both higher than high-grade glioma. The Deek's plot showed no significant publication bias (t = −1.03, P = 0.33). Intraoperative ultrasound has high overall diagnostic value to identify glioma remnants, especially in low-grade glioma, which shows a benefit for prognosis and life quality of patients. In general, Intraoperative ultrasound is an effective tool for maximizing the extent of glioma resection.