Miracle-dz/UniFAR-FTUs huggingface dataset:
First experimental charge density study using a Bruker CMOS-type PHOTON 100 detector: the case of ammonium tetraoxalate dihydrate. Addendum.

The aim of this study was to test the applicability of a Bruker AXS CMOS-type PHOTON 100 detector for the purpose of a fine charge density quality data collection. A complex crystal containing oxalic acid, ammonium oxalate and two water molecules was chosen as a test case. The data was collected up to a resolution of 1.31 A−1 with high completeness (89.1%; Rmrg = 0.0274). The multipolar refinement and subsequent quantum theory of atoms in molecules (QTAIM) analysis resulted in a comprehensive description of the charge density distribution in the crystal studied. The residual density maps are flat and almost featureless. It was possible to derive reliable information on intermolecular interactions to model the anharmonic motion of a water molecule, and also to observe the fine details of the charge density distribution, such as polarization on O and H atoms involved in the strongest hydrogen bonds. When compared with our previous statistical study on oxalic acid data collected with the aid of CCD cameras, the complementary metal-oxide semiconductor (CMOS) detector can certainly be classified as a promising alternative in advanced X-ray diffraction studies.
Live Attenuated Influenza Virus Expressing Human Interleukin-2 Reveals Increased Immunogenic Potential in Young and Aged Hosts

ABSTRACT Despite the reported efficacy of commercially available influenza virus vaccines, a considerable proportion of the human population does not respond well to vaccination. In an attempt to improve the immunogenicity of live influenza vaccines, an attenuated, cold-adapted (ca) influenza A virus expressing human interleukin-2 (IL-2) from the NS gene was generated. Intranasal immunization of young adult and aged mice with the IL-2-expressing virus resulted in markedly enhanced mucosal and cellular immune responses compared to those of mice immunized with the nonrecombinant ca parent strain. Interestingly, the mucosal immunoglobulin A (IgA) and CD8+ T-cell responses in the respiratory compartment could be restored in aged mice primed with the IL-2-expressing virus to magnitudes similar to those in young adult mice. The immunomodulating effect of locally expressed IL-2 also gave rise to a systemic CD8+ T-cell and distant urogenital IgA response in young adult mice, but this effect was less distinct in aged mice. Importantly, only mice immunized with the recombinant IL-2 virus were completely protected from a pathogenic wild-type virus challenge and revealed a stronger onset of virus-specific CD8+ T-cell recall response. Our findings emphasize the potential of reverse genetics to improve the efficacy of live influenza vaccines, thus rendering them more suitable for high-risk age groups.
Feeding the Person With Late-Stage Alzheimer's Disease

Families need guidance in making decisions on how to feed a loved one with late-stage Alzheimer’s disease. Tube feedings have not been shown to extend life, improve nutritional status, or reduce pressure sores or aspiration and may have some negative effects on quality of life. Even so, they continue to be used widely. Assisted feeding may be an appropriate method when the therapeutic goal is comfort feeding. Resistance by health care professionals and surrogate decision makers to ‘‘withholding food’’ from a person with late dementia can be reduced with education. Nutr Today. 2011;46(2):75–79
Youths and HIV/AIDS: psychiatry's role in a changing epidemic.

OBJECTIVE To review the past 10 years of published research on human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) in the United States, including psychosocial and psychiatric risk factors, epidemiology, biology, neurocognitive and psychiatric sequelae, disclosure issues, prevention strategies, and biological and behavioral treatments. METHOD Researchers reviewed the English-language literature with a focus on child and adolescent risk factors associated with HIV/AIDS, prevention, and treatment. RESULTS Substantial scientific advances have occurred over the past two decades leading to decreased morbidity and mortality in the United States from AIDS-related opportunistic infections. At the same time, rates of HIV infection are increasing in teenagers, young women, and minorities, and growing numbers of youths are living with an infected family member. Understanding HIV risk behavior requires a broad theoretical framework. Comprehensive HIV prevention programs have led to reduced risk behavior among HIV-affected youths and teens at risk of infection. Biological and behavioral treatments of HIV infection continue to evolve and have led to longer life span, improved quality of life, and fewer psychiatric problems. CONCLUSIONS HIV/AIDS has significant mental health implications, and psychiatry can play a critical role in curbing the epidemic. With minimal effort, mental health professionals can adapt and apply the strategies that they use to treat psychiatric symptoms to prevent HIV transmission behaviors.
Analysis of peptides using N‐methylpolyvinylpyridium as silica surface modifier for CE‐ESI‐MS

In this study, the N‐methylpolyvinylpyridinuim polymer has for the first time been used as a silica surface modifier for CE in combination with ESI MS (CE‐ESI‐MS). The compatibility for ESI‐MS was demonstrated by the analysis of peptides and protein digests. The N‐methylpolyvinylpyridium surface interacts electrostatically with the ionized silanol groups, giving a cationic surface with a reversed EOF. The surface modifier gave rapid and repeatable separations of peptides, proteins and protein digests at acidic pH for more than 4 h of continuous use. The CE separation yielded peak efficiencies of up to 4.3×105 plates/m. The surface coating is highly compatible with ESI and facilitates the separation and analysis of complex peptide mixtures as shown by the analysis of BSA digests.
Molecular classification of thyroid nodules using high-dimensionality genomic data.

OBJECTIVE We set out to develop a molecular test that distinguishes benign and malignant thyroid nodules using fine-needle aspirates (FNA). DESIGN We used mRNA expression analysis to measure more than 247,186 transcripts in 315 thyroid nodules, comprising multiple subtypes. The data set consisted of 178 retrospective surgical tissues and 137 prospectively collected FNA samples. Two classifiers were trained separately on surgical tissues and FNAs. The performance was evaluated using an independent set of 48 prospective FNA samples, which included 50% with indeterminate cytopathology. RESULTS Performance of the tissue-trained classifier was markedly lower in FNAs than in tissue. Exploratory analysis pointed to differences in cellular heterogeneity between tissues and FNAs as the likely cause. The classifier trained on FNA samples resulted in increased performance, estimated using both 30-fold cross-validation and an independent test set. On the test set, negative predictive value and specificity were estimated to be 96 and 84%, respectively, suggesting clinical utility in the management of patients considering surgery. Using in silico and in vitro mixing experiments, we demonstrated that even in the presence of 80% dilution with benign background, the classifier can correctly recognize malignancy in the majority of FNA samples. CONCLUSIONS The FNA-trained classifier was able to classify an independent set of FNAs in which substantial RNA degradation had occurred and in the presence of blood. High tolerance to dilution makes the classifier useful in routine clinical settings where sampling error may be a concern. An ongoing multicenter clinical trial will allow us to validate molecular test performance on a larger independent test set of prospectively collected thyroid FNAs.
The Suppressor of Cytokine Signaling (SOCS) 1 and SOCS3 but Not SOCS2 Proteins Inhibit Interferon-mediated Antiviral and Antiproliferative Activities*

The suppressor of cytokine signaling (SOCS) proteins are a family of cytokine-inducible negative regulators of cytokine signaling. Interferon (IFN)-γ treatment induces the expression of SOCS1, SOCS2, and SOCS3 mRNAs. To examine the effect of SOCS proteins on IFN-mediated Janus-activated kinase/signal transducers and activators of transcription (STAT) signaling, HeLa- and MCF-7-derived stable cell lines expressing SOCS1, SOCS2, and SOCS3 proteins were established. SOCS1 and SOCS3 but not SOCS2 inhibited the tyrosine phosphorylation and nuclear translocation of STAT1 in response to IFN stimulation. The IFN-mediated antiviral and antiproliferative activities were consistently blocked by the constitutive expression of SOCS1 and SOCS3 but not SOCS2 proteins. The maximum inhibitory activities of SOCS1 and SOCS3 proteins toward the activation of STAT1 were observed at very low levels of SOCS protein expression. In addition, SOCS1 exhibited a much stronger inhibitory activity toward the activation of STAT1 than did SOCS3. These results suggest that SOCS1 and SOCS3 but not SOCS2 are inhibitors of IFN-mediated Janus-activated kinase/STAT signaling pathways.
Neuromuscular and inflammatory responses to handball small‐sided games: the effects of physical contact

The aim of this study was to investigate the influence of physical contact on neuromuscular impairments and inflammatory response during handball small‐sided games. Using a counterbalanced design, 12 elite male junior handball players were divided into two groups: contact (C‐SSG) and no‐contact (NC‐SSG), performing both contact and no‐contact small‐sided games, in reverse order on two training sessions separated by 5 days. The methodology and rules were identical for the two SSG regimens, with the only difference being the inclusion or prohibition of upper body use for physical contacts. Upper and lower body neuromuscular performances and blood concentrations of inflammatory cytokine IL‐6 were assessed before and immediately after the games. During small‐sided games, video analysis was used to establish the physical contact counts. Significant differences were found in most upper and lower limbs muscles kinetic variables and in the physical contact events (all P < 0.001) following the two training regimens. There was an increase in IL‐6 after C‐SSG and no changes following NC‐SSG (P < 0.05 and P = 0.12, respectively). Moreover, a strong correlation was found between the number of physical contacts and IL‐6 responses (r = 0.971, P < 0.001) in C‐SSG. This study indicates that an inflammatory response and large upper and lower body neuromuscular impairments result from physical contact in elite handball players. These outcomes outline the specific physiological profile of C‐SSG that, in turn, might be used by practitioners and coaches as a practical approach to strategically select exercises in athlete's overall training program.
Analysis of the Achievable Rate for a Multiuser System with Multiple Antennas

This paper investigates the performance of a multi user system where nodes, which are supposed to be uniformly and randomly distributed in a given area, transmit information to a base station which is equipped with smart antennas. In the paper herein we evaluate the achievable rate at the base station by considering the effect of propagation and nodes' location. We derive a lower bound as well as an approximate expression for the mean achievable rate. The lower bound requires the calculation of one single integral whereas the approximation is expressed in closed form and is valid for an arbitrary number of nodes and receiving antennas at the base station.
[Qualitative and quantitative determination of the main components of huanglianjiedu decoction by HPLC-UV/MS].

AIM To establish a comprehensive HPLC analytical method of Huanglianjiedu decoction. METHODS This study was performed by HPLC-UV/MS to identify the chemical constituents of the whole and individual herbs of the "Huanglianjiedu decoction". Zorbax Extend C18 (150 mm x 4. 6 mm ID, 5 microm) column was used; the mobile phase was composed of acetonitrile (A) and water (B, with 0.5% acetic acid) with gradient elution; the flow rate was 1.0 mL x min(-1) and the column temperature was setup at 25 degrees C. The detection wavelength was 254 nm. RESULTS The chromatogram of Huanglianjiedu decoction showed 21 main peaks. Peaks 1, 2, 5 and 18 were from Gardenia jasminoides Ellis, Peaks 8, 13, 14, 15, 16, 17, 19 and 21 from Scutellaria baicalensis Georgi. While 10 from Coptis chinensis Franch and 20 from Phellodendron amurense Rupr. , Peaks 3, 4, 6, 9, 11 and 12 came from them together. Peak 7 presented in the chromatograms of the herbs except Gardenia jasminoides Ellis. By comparison of the retention time, the on-line UV spectra and MS spectra, 11 peaks were identified as 5 (geniposide), 9 (jatrorrhizine), 10 (coptisine), 11 (palmatine), 12 (berberine), 13 (baicalin), 15 (oroxin A), 17 (wogonoside), 19 (baicalein), 20 (obaculactone), 21 (wogonin), then eight of them were quantified by HPLC-UV. CONCLUSION The method could represent the characteristics of Huanglianjiedu decoction, and it could be used to evaluate the quality and quantity of Huanglianjiedu decoction. It distinguished between Coptis chinensis Franch and Phellodendron amurense Rupr. by HPLC for the first time.
Implicit Learning of Second-, Third-, and Fourth-Order Adjacent and Nonadjacent Sequential Dependencies

Serial reaction time (SRT) task studies have established that people can implicitly learn first- and second-order adjacent dependencies. Sequential confounds have made it impossible to draw conclusions regarding learning of nonadjacent dependencies and learning of third- and fourth-order adjacent dependencies. Addressing the confounds, the present study shows that people can implicitly learn second-, third-, and fourth-order adjacent and nonadjacent dependencies embedded in probabilistic sequences of target locations.
An Off-Line Cursive Handwriting Recognition System

Describes a complete system for the recognition of off-line handwriting. Preprocessing techniques are described, including segmentation and normalization of word images to give invariance to scale, slant, slope and stroke thickness. Representation of the image is discussed and the skeleton and stroke features used are described. A recurrent neural network is used to estimate probabilities for the characters represented in the skeleton. The operation of the hidden Markov model that calculates the best word in the lexicon is also described. Issues of vocabulary choice, rejection, and out-of-vocabulary word recognition are discussed.
Modeling 1H exchange: An estimate of the error introduced in MRI by assuming the fast exchange limit in bolus tracking

A simulation is presented which calculates the MRI signal expected from a model tissue for a given pulse sequence after a bolus injection of a contrast agent. The calculation assumes two physiologic compartments only, the intravascular and extravascular spaces. The determination of the concentration of contrast in each compartment as a function of time and position has been outlined in a previous publication (Moran and Prato, Magn Reson Med 2001;45:42–45). These contrast agent concentrations are used here to determine the NMR relaxation times as a function of time and position within the tissue. Knowledge of this simulated tissue ‘map’ of relaxation times as a function of time provides the information required to determine whether the proton exchange rate is fast or slow on the NMR timescale. Since with a bolus injection the concentration of contrast and hence the relaxation time may vary with position along the capillary, some segments of the capillary are allowed to be in fast exchange with the extravascular space, while others may be in slow exchange. Using this information, and parameters specific to a given tissue, the MRI signal for a given pulse sequence is constructed which correctly accounts for differences in proton exchange across the length of the capillary. It is shown that extravascular contrast agents show less signal dependence on water exchange, and thus may be more appropriate for quantitative imaging when using fast exchange assumptions. It is also shown that nondistributed compartment models can incorrectly estimate the water exchange that is occurring at the capillary level if exchange‐minimizing pulse sequences are not used. Magn Reson Med 51:816–827, 2004. © 2004 Wiley‐Liss, Inc.
Computational investigation of fluid velocity in a biochip microchannel for single cell trapping

A highly requirement of analyzing a biological sample at a so-called single cell level has encouraged for the development of innovative and versatile microdevices. Up to now, microfluidic devices have become as emerging technologies that can support an investigation and analysis of a living cell. For many cuttingedge single cell studies, trapping of individual cells at specific locations in the developed microfluidic device is truly essential prior to characterization or quantification of cells biophysical properties. In this paper, microfluidic devices capable of trapping a single cell are designed simply through a concept of hydrodynamic manipulation. The microfluidic devices are designed with a series of trap and bypass microchannel structures for trapping individual cells without the need for microwell, robotic equipment, external electric force or surface modification. Two designs of microchannel: 1) Loop-type and 2) T-type are proposed. In order to investigate the single cell trapping capability, a finite element model of the proposed design have been developed using ABAQUS-FEA software in which the fluid velocity can be analyzed. Based on the simulation, the geometrical parameters which affect the single cell trapping are appropriately selected. After adapting the trap and bypass microchannel structures via simulations, a single cell can be trapped at a desired location efficiently. It is shown that the simulation results are in a good agreement with the previously reported experimental studies. Index Terms — Microfluidic, Biochip, Cell Trapping, Hydrodynamic, Finite Element Simulation.
Exploiting Document Level Semantics in Document Clustering

Document clustering is an unsupervised machine learning method that separates a large subject heterogeneous collection (Corpus) into smaller, more manageable, subject homogeneous collections (clusters). Traditional method of document clustering works around extracting textual features like: terms, sequences, and phrases from documents. These features are independent of each other and do not cater meaning behind these word in the clustering process. In order to perform semantic viable clustering, we believe that the problem of document clustering has two main components: (1) to represent the document in such a form that it inherently captures semantics of the text. This may also help to reduce dimensionality of the document and (2) to define a similarity measure based on the lexical, syntactic and semantic features such that it assigns higher numerical values to document pairs which have higher syntactic and semantic relationship. In this paper, we propose a representation of document by extracting three different types of features from a given document. These are lexical , syntactic and semantic features. A meta-descriptor for each document is proposed using these three features: first lexical, then syntactic and in the last semantic. A document to document similarity matrix is produced where each entry of this matrix contains a three value vector for each lexical , syntactic and semantic . The main contributions from this research are (i) A document level descriptor using three different features for text like: lexical, syntactic and semantics. (ii) we propose a similarity function using these three, and (iii) we define a new candidate clustering algorithm using three component of similarity measure to guide the clustering process in a direction that produce more semantic rich clusters. We performed an extensive series of experiments on standard text mining data sets with external clustering evaluations like: FMeasure and Purity, and have obtained encouraging results.
Removal of pharmaceuticals in biologically treated wastewater by chlorine dioxide or peracetic acid

Removal of six active pharmaceutical ingredients in wastewater was investigated using chlorine dioxide (ClO2) or peracetic acid (PAA) as chemical oxidants. Four non-steroidal anti-inflammatory drugs (ibuprofen, naproxen, diclofenac and mefenamic acid) and two lipid-regulating agents (gemfibrozil and clofibric acid, a metabolite of clofibrate) were used as target substances at 40 μg/L initial concentration. Three different wastewaters types originating from two wastewater treatment plants (WWTPs) were used. One wastewater was collected after extended nitrogen removal in activated sludge, one after treatment with high-loaded activated sludge without nitrification, and one from the final effluent from the same plant where nitrogen removal was made in trickling filters for nitrification and moving-bed biofilm reactors for denitrification following the high-loaded plant. Of the six investigated compounds, only clofibric acid and ibuprofen were not removed when treated with ClO2 up to 20 mg/L. With increasing PAA dose up to 50 mg/L, significant removal of most of the pharmaceuticals was observed except for the wastewater with the highest chemical oxygen demand (COD). This indicates that chemical oxidation with ClO2 could be used for tertiary treatment at WWTPs for active pharmaceutical ingredients, whereas PAA was not sufficiently efficient.
A Comparison of Catch Trial Methods Used in Standard Automated Perimetry in Glaucoma Patients

PurposeTo compare the false-positive (FP) response rates between 2 methods used by the Humphrey Field Analyzer in glaucoma patients. MethodsOne eye of one hundred and twenty glaucoma patients was tested twice within 2 months with 24-2 SITA Standard and 24-2 full threshold (FT) perimetric test procedures. FP rates were obtained with the response time window (RTW) method used by SITA and the blank presentation (BP) method of the size V FT procedure. False-negative (FN) catch trial rates were also examined. A repeated measure, 2×2 analysis of variance was used to examine error rates, and FP rates for visits 1 and 2 were regressed to investigate its relationship. ResultsFor FP rates on the first 2 visits, glaucoma patients had no significant differences comparing RTW (SITA) with BP (FT) (1.99% vs. 1.88%) and higher mean FN rates (4.11% vs. 1.69%, P=0.001); the FP rates at visit 2 were similar (1.69% vs. 2.08%) and FN rates were lower for both methods at visit 2. However, when comparing patients with FP responses that occurred with both RTW and BP methods, RTW rates were lower (3.58% vs. 7.72%, P=0.007). ConclusionsThe RTW method seems to underestimate FP response rates.