Miracle-dz/UniFAR-FTUs huggingface dataset:
One degree of freedom for dominance in indirect association studies

Usual tests of association using tag single nucleotide polymorphisms (SNPs) assume that the alleles of the causal locus act additively and that these alleles are then predicted indirectly via a set of tag SNPs. In the presence of strong dominance effects this model is not correct and an extra term needs to be included, which uses the tag SNPs to predict the heterozygosity of the causal locus. Assuming this scenario of a strong dominance effect, we present an appropriate test statistic and investigate how much power, if any, we gain by adding this single degree of freedom for dominance. Genet. Epidemiol. 2007. © 2007 Wiley‐Liss, Inc.
The Chemistry of Atmosphere-Forest Exchange (CAFE) Model – Part 2: Application to BEARPEX-2007 observations

In a companion paper, we introduced the Chemistry of Atmosphere-Forest Exchange (CAFE) model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. Here, we apply CAFE to noontime observations from the 2007 Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX-2007). In this work we evaluate the CAFE modeling approach, demonstrate the significance of in-canopy chemistry for forest-atmosphere exchange and identify key shortcomings in the current understanding of intra-canopy processes. CAFE generally reproduces BEARPEX-2007 observations but requires an enhanced radical recycling mechanism to overcome a factor of 6 underestimate of hydroxyl (OH) concentrations observed during a warm (~29 °C) period. Modeled fluxes of acyl peroxy nitrates (APN) are quite sensitive to gradients in chemical production and loss, demonstrating that chemistry may perturb forest-atmosphere exchange even when the chemical timescale is long relative to the canopy mixing timescale. The model underestimates peroxy acetyl nitrate (PAN) fluxes by 50% and the exchange velocity by nearly a factor of three under warmer conditions, suggesting that near-surface APN sinks are underestimated relative to the sources. Nitric acid typically dominates gross dry N deposition at this site, though other reactive nitrogen (NO_y) species can comprise up to 28% of the N deposition budget under cooler conditions. Upward NO_2 fluxes cause the net above-canopy NO_y flux to be ~30% lower than the gross depositional flux. CAFE under-predicts ozone fluxes and exchange velocities by ~20%. Large uncertainty in the parameterization of cuticular and ground deposition precludes conclusive attribution of non-stomatal fluxes to chemistry or surface uptake. Model-measurement comparisons of vertical concentration gradients for several emitted species suggests that the lower canopy airspace may be only weakly coupled with the upper canopy. Future efforts to model forest-atmosphere exchange will require a more mechanistic understanding of non-stomatal deposition and a more thorough characterization of in-canopy mixing processes.
[Application of Berlin questionnaire in the screening of obstructive sleep apnea hypopnea syndrome].

OBJECTIVE To investigate the value of Berlin questionnaire in screening obstructive sleep apnea hypopnea syndrome (OSAHS) among Chinese. METHODS A total of 302 cases with suspected OSAHS were referred to our sleep laboratory. The Berlin questionnaire scores and polysomnography (PSG) monitoring data were analyzed. According to the Berlin questionnaire score, the patients were divided into high and lower risk groups for OSAHS. In terms of the PSG monitoring results, the patients were classified into non-OSAHS, mild, moderate and severe OSAHS groups. The age, gender, apnea hypopnea index (AHI), body mass index, and the Berlin questionnaire (BQ) result were compared among the 4 groups. The correlation of Berlin questionnaire result with age, AHI, the lowest SpO2 (LSpO2) and microarousal index (MAI) were analyzed. RESULTS There were significant differences in the Berlin questionnaire results among non-OSAHS and the other 3 groups (χ(2) = 13.961, 8.466, 42.156, P < 0.0083); and between the severe OSAHS and the other 2 groups (χ(2) = 9.439, 11.162, P < 0.0083). There was no statistical difference between the mild and moderate groups (P > 0.0083). The ratio of the high BQ risk patients had an increasing tendency as the severity of OSAHS was increased (χ(2) = 34.211, P < 0.01). The Berlin questionnaire results showed a positive correlation with age, AHI or MAI (r = 0.125, 0.346, 0.198, all P < 0.05, respectively) but a negative correlation with LSpO2 (r = -0.371, P < 0.01). The Berlin questionnaire results showed no correlation with gender (P > 0.05). The sensitivity and the specificity of the Berlin questionnaire in predicting sleep apnea were 0.71 and 0.72, respectively. CONCLUSIONS With the moderate sensitivity and the specificity, the Berlin questionnaire has some value in screening patients with OSAHS. However, it is not correlated with the severity of OSAHS in Chinese patients. Thus Berlin questionnaire has limited value in the screening of OSAHS among Chinese.
Batch fabrication of carbon nanotubes at AFM probe tips and AFM imaging

We synthesized carbon nanotubes (CNTs) at the tips of commercial atomic force microscope (AFM) probes by chemical vapor deposition (CVD) process with applying an electric field. Applying the electric field during the CVD process increased the yield of AFM probes with CNTs at the tips (CNT-AFM probes). We formed a catalyst layer on the surface of AFM probes, and carried out the CVD process to synthesize CNTs. After the CVD process, we observed the tips of the AFM probes with a scanning electron microscope (SEM). The yield of CNT-AFM probes was about 52 %. The CNTs were determined by resonance Raman spectroscopy using a 488 nm argon ion laser. Observed Raman peaks were peculiar to single-walled carbon nanotubes (SWNTs). Then we obtained AFM images of a sample grating with the CNT-AFM probes. The CNT-AFM probes had higher horizontal resolution than standard commercial AFM probes.
Can cytomorphology of granulomas distinguish sarcoidosis from tuberculosis? Retrospective study of endobronchial ultrasound guided transbronchial needle aspirate of 49 granulomatous lymph nodes

Background: The differential diagnosis of tuberculosis (TB) and sarcoidosis on fine needle aspiration material is very challenging in tubercular endemic regions. We carried out a pilot study to explore cytomorphologic features of granulomas which could help in differentiation between sarcoidosis and TB. Final diagnoses in these patients were based on clinical, microbiologic and follow-up studies. Materials and Methods: Endobronchial ultrasound guided transbronchial needle aspiration smears of 49 consecutive patients with a final cytologic diagnosis of granulomatous lymphadenitis were reviewed. Based on cytologic features two cytologic categories were enunciated and the results were correlated with microbiologic studies and/follow-up of minimum of 6 months. Results: The cytologic categories did not correlate with the final clinical outcome of patients. Conclusions: Different patterns of granulomas observed in cytology smears do not help distinguish TB from sarcoidosis. The novel non-invasive techniques of mediastinal sampling though help in confirming granulomatous pathology, distinction between these entities and treatment decisions still depend upon correlating cytologic, microbiologic, clinical and radiological data in a large number of cases in tubercular endemic regions.
Clinicopathological profile of gastrointestinal lymphomas in Kashmir

Abstract Background: The histological categorization of lymphoma has been a source of controversy for many years for both clinicians and pathologists. Clinicopathologic information of gastrointestinal lymphomas in Indian subcontinent is lacking. We studied histopathological spectrum of Primary Gastrointestinal Lymphomas (PGIL) and attempted to classify the G.I. lymphomas based on the recent WHO classification in to major histological types and immunological categories. Material and Methods: This study was done to evaluate the clinicopathological pattern of 100 cases with a histopathological diagnosis of primary gastrointestinal lymphoma at a tertiary care hospital. All patients of primary gastrointestinal lymphomas were included with the help of medical records over a 11-years period that is, January 2005 to December 2015. Results: The study included 100 cases (60 males, 40 females; mean age 51.43 years; age range 4.5-90 years) . The disease involved stomach in 82 (82%), small intestine in 8 (8%), large bowel and rectum in 8 (8%), gall bladder in 1 (1%) and oesophagus in 1 (1%). 82 (82%) of the 100 cases were Diffuse Large B cell lymphomas; 12 (12%) were Extra Nodal Marginal Zone Lymphomas (ENMZL of MALT type) 2 (2%) IPSID 2 (2%) of Mantle cell lymphoma morphology, 1 (1%) Burkitt's and 1(1%) enteropathy associated T cell lymphoma. The commonest presenting symptom was abdominal pain. 99 (99%) of 100 tumours were classified as B-cell lymphomas immunohistochemically and majority exhibited monoclonal light chain restriction on kappa/lambda staining. In addition; Burkitt's lymphoma showed positivity for CD 10. One tumour (1%) showed positivity for T-cell markers. The data demonstrated that primary GI NHL is more common among males, mainly in their fifth decade. Abdominal pain is the most common presenting symptom, with stomach being the most commonly involved site. Diffuse large cell lymphoma is the most frequent histologic subtype, followed by extranodal marginal-zone B cell lymphoma (MALT type). H. Pylori infection was observed in cases with low grade MALT lymphomas. Striking was the observation of two cases of IPSID (a disease commonly found in Mediterranean countries) and one case of enteropathy associated T cell lymphoma. Conclusion: EGD, imaging, light microscopic examination and immunohistochemical workup for B and T cell markers and staining for light chains to assist documentation of monoclonality are of precise diagnostic value in gastrointestinal lymphomas and form a part of the diagnostic workup.
Validation of a Commercially Available Monoclonal Antibody-Based Competitive-Inhibition Enzyme-Linked Immunosorbent Assay for Detection of Serum Antibodies to Neospora caninum in Cattle

ABSTRACT A previously described monoclonal antibody (MAb)-based competitive-inhibition enzyme-linked immunosorbent assay (cELISA) was modified to optimize performance, and the assay was validated in various defined cattle populations for detection of serum antibody to Neospora caninum, a major cause of bovine abortion. Modifications to the cELISA included capturing nativeN. caninum antigen with a parasite-specific MAb (MAb 5B6-25) and directly conjugating the competitor MAb (MAb 4A4-2), with both MAbs binding different epitopes of a conserved, immunodominant 65-kDa tachyzoite surface antigen. The assay was validated using three serum sets, a “gold standard” set of 184 cow sera defined by fetal histopathology and N. caninum immunohistochemistry and by maternal N. caninum indirect fluorescence assay (IFA) at a 1:200 serum dilution, a relative standard set of 330 cow sera defined by IFA alone, and a set of 4,323 cow sera of unknown N. caninum status. A test cutoff of 30% inhibition was identified. The diagnostic sensitivity was 97.6%, and diagnostic specificity was 98.6% for the gold standard abortion-defined sera. The diagnostic sensitivity was 96.4%, and diagnostic specificity was 96.8% for the relative standard IFA-defined sera. Testing of the 4,323 bovine sera of unknown N. caninum status revealed a distinct bimodal distribution and steep sigmoid frequency curve with only 1.8% of samples within 5% of the test cutoff, indicating a sharp discrimination between test-positive and test-negative samples. In summary, the modified N. caninum cELISA provided a simple, rapid, and versatile method to accurately identify N. caninum infection status in cattle using a single cutoff value.
Zero temperature coefficient gas-sealed pressure sensor using mechanical temperature compensation

A novel gas sealed capacitive pressure sensor with a self-temperature compensated structure is reported. The pressure sensor is sealed by Au-Au diffusion bonding in nitrogen with a pressure of 100 kPa and integrated with a platinum resistor based temperature sensor for human activity monitoring. A ring-shaped structure on the diaphragm of the pressure sensor is used for temperature compensation. The pressure sensor with the temperature compensation structure can mechanically suppress the thermal expansion effect of the sealed gas in cavity. Using the compensation structure, measured temperature coefficient was much reduced as compared to that of the pressure sensor without compensation. The sensitivities of the pressure sensor before and after compensation are almost same in a pressure range from 80 kPa to 100 kPa.
Redundancy Reduction in ASR of Spontaneous Speech Through Statistical Machine Translation

This paper describes a system, based on statistical machine translation, that tries to remove from the output of an automatic audio transcription system non relevant words, such as: erroneously inserted functional words, ﬁlled pauses, interjections, word fragments, etc, as well as to repair, at a certain extent, ungrammatical pieces of sentences. For this work 1 we decided to concentrate on a political speeches application domain, due to the immediate availability of a parallel corpus of automatic audio transcriptions and related proceedings, manually produced. The system can effectively detect and correct several errors (mainly insertions) included in the alignment between a given automatic audio transcription and a reference transcription derived from a corresponding proceeding. Preliminary results, expressed in terms of word error rate, show that the proposed approach allows to improve of a relative 5% with respect to the usage of the pure automatic transcription of the audio.
Automatic speaker verification experiments using HMM

This paper addresses the design and implementation of automatic speaker verification (ASV) systems. There is great interest in developing and increasing the performance of ASV applications, taking into account the advantages offered when compared to other biometrical methods. State-of-the-art speaker recognizers are based on statistical models such as GMM, HMM, SVM, ANN or hybrid models. This work reports experiments on prompted text speaker verification on a Romanian corpus. First, a Hidden Markov Model (HMM) based continuous speech recognizer is built at context independent, single mixture, monophone level. Then the client model and the world model are built using appropriate speech data. The text-prompted speaker verification system is based on sentence HMMs, constructed for the key text by concatenating corresponding acoustic models. In the verification stage, the normalized log-likelihood is derived as the difference between the log-likelihood obtained through Viterbi forced alignment of the client model and world model, respectively. Finally a procedure used to determine the verification performances is presented.
Selecting Trustworthy Content using Tags

Networked portable devices enable their users to easily create and share digital content (e.g., photos, videos). Hitherto, this serendipitous form of sharing has not happened. That may be because, for sharing content, mobile users have no choice but to go through the Internet. Users are thus in need of decentralised mechanisms for browsing location-based content. To realize such mechanisms, the following two questions must be answered first: how to select "relevant content", by semantically matching user queries, and how to select "quality content" from the clutter generated by a potentially huge number of producers. We explore ways to answer these questions. We propose a combined approach that infers "relevance" by reasoning about the semantics emerging from the tags that users associate to content, and "quality" by running distributed trust models that recognize trustworthy producers.
FRPCA: Fast Robust Principal Component Analysis for online observations

While the performance of Robust Principal Component Analysis (RPCA), in terms of the recovered low-rank matrices, is quite satisfactory to many applications, the time efficiency is not, especially for scalable data. We propose to solve this problem using a novel fast incremental RPCA (FRPCA) approach. The low rank matrices of the incrementally-observed data are estimated using a convex optimization model that exploits information obtained from the preestimated low-rank matrices of the original observations. The evaluation results supports the potential of FRPCA for fast, yet accurate, recovery of the low-rank matrices. The proposed FRPCA boosts the efficiency of the traditional RPCA by multiple hundreds of times, while scarifying less than 1% of accuracy.
The Effect of Investment Promotion on Foreign Direct Investment Inflow into Ghana

The paper investigated the effect of investment promotion (IP) on foreign direct investment flow (FDI) into Ghana. Cointegration among the variables was established using auto regressive distributed lag (ARDL) models in the presence of a mix of I (0) and I (1) variables. The control variables, inflation and trade openness were statistically significant in the short run. Whilst inflation exerted a negative effect on FDI inflow; trade openness positively induced FDI inflow. GDP per capita and exchange rate did not statistically significantly influence FDI inflow in the short run. In respect of the key variable GIPC, in the short run, there was a positive but statistically insignificant effect on FDI inflow. The estimated long-run ARDL model showed that macroeconomic variables such as inflation, GDP and trade openness determined FDI inflow into Ghana. Notwithstanding the positive relationship between establishment of IP agency (GIPC) and FDI inflow, this relationship was statistically insignificant. Greater efforts at macroeconomic management specifically, promotion of external trade, increasing GDP and reducing inflation holds more promise to attracting FDI into Ghana. GIPC should be maintained to provide a supportive role when the foreign investors arrive in Ghana.
Influence of non-structural infill wall elements on the seismic response and retrofit of steel structures

This work provides a methodology for evaluating the influence of non-structural infill wall elements and quantifying the interrelation between them and structural damage analytically evaluated under strong ground motions. For this reason, nonlinear dynamic analyses for a set of five steel frame structures were carried out taking into consideration all essential material characteristics as well as four different infill wall topologies. Initially, a set of spectrum compatible artificial accelerograms were composed, and nonlinear dynamic analyses have been carried out to evaluate the seismic response of each structure. From several structural response quantities, the overall structural damage index (OSDI) of Park/Ang (OSDIPA) has been selected to represent the structural response. The work focuses on damage index of Park/Ang (DIPA) in both its localized form as well as the global damage manifestation. The steel frame models were designed in compliance with EC3 and EC8 Eurocode requirements for steel and antiseismic structures, respectively. During the nonlinear dynamic analyses carried out to evaluate the structure’s seismic response, utilizing the IDARC computer program, the OSDIPA response parameters were calculated as simple, yet efficient and widely accepted ways to represent seismic damage. This work focus on quantifying the interdependency between the topology of infill walls in a steel structure and its seismic response. As the numerical results have shown, infill walls proved to have a very positive contribution to the structure’s seismic response giving an average of 47% reduction of the maximum recorded OSDIPA as well as a 72-81% decrease in the mean OSDIPA values between the bare frame structure and its infill wall reinforced counterparts. Similar results were observed on a localized basis when investigating the mode and structural damage accumulation on a level to level basis where reductions in the range of 68-82% of the mean values for the ground floor (Level 1) and almost eliminate the seismic damage that is observed on the bare frame’s Level 6. Finally, a comparative study has been performed to quantify the influence of non-structural infill wall topology on the analytically observed seismic induced structural damage. In that effect, the different damage distribution characteristics have been studied revealing the importance of non-structural elements in a building’s response to such conditions.
5-HTTLPR Polymorphism: Analysis in South African Autistic Individuals

Abstract The serotonin transporter promoter length polymorphism (5-hydroxytryptamine transporter length polymorphism; 5-HTTLPR) has long been implicated in autism and other psychiatric disorders. The use of selective serotonin reuptake inhibitors (SSRIs) has a positive effect on treating some symptoms of autism. The effects of these drugs vary in individuals because of the presence of the S or L allele of 5-HTTLPR. Studies performed on various autistic populations have found different allele frequencies for the L and S alleles. Allele frequencies and genotypes of the South African autistic populations (African, mixed, and Caucasian) were compared with matching South African ethnic control populations. The *S/*S genotype was found to be highly significantly associated with all the South African autistic ethnic populations. In the South African African population the *S/*S genotype was present in 7 (33%) of the autistic individuals but in none of the control subjects, yielding infinitely large odds of developing autism. The odds of developing autism with the *S/*S genotype compared to the *L/*L genotype increased 10.15-fold in the South African mixed group and 2.74-fold in the South African Caucasian population. The allele frequency of the South African autistic population was also compared with studies of other autistic populations around the world, and highly significant differences were found with the Japanese, Korean, and Indian population groups. The difference was not significant for the French, German, Israeli, Portuguese, and American groups. This is the first South African study of autistic individuals of different ethnic backgrounds that shows significant differences in allele and genotype frequencies of 5-HTTLPR. The results of this study open new avenues for investigating the role of transmission of the L and S alleles in families with autism in South Africa.
Nephrocalcinosis: new insights into mechanisms and consequences.

The most common form of renal stone disease, calcium nephrolithiasis, is defined as the presentation of a macroscopic concrement of inorganic (calcium phosphate and/or calcium phosphate) and organic material in the renal calyces and/or pelvis, either adhered to the papillae or pelvic urothelium or not. In search of the mechanism underlying calcium nephrolithiasis, in vitro and in vivo studies and observations in human biopsies have shown the presence of two distinct types of renal microscopical crystal deposition processes; one taking place within the tubular lumen (intratubular nephrocalcinosis), and the other in the interstitium (interstitial nephrocalcinosis). Recent observations, however, strongly suggest that nephrocalcinosis and calcium nephrolithiasis are to be considered two independent pathologies and that nephrocalcinosis may cause calcium nephrolithiasis only in particular conditions. In this review, we discuss our current understanding of the mechanisms involved in both types of nephrocalcinosis (intratubular and interstitial), their possible consequences and their relation to calcium nephrolithiasis.