Miracle-dz/UniFAR-FTUs huggingface dataset:
The occurrence of CH…O hydrogen bonds in α‐helices and helix termini in globular proteins

A comprehensive database analysis of CH…O hydrogen bonds in 3124 α‐helices and their corresponding helix termini has been carried out from a nonredundant data set of high‐resolution globular protein structures resolved at better than 2.0 Å in order to investigate their role in the helix, the important protein secondary structural element. The possible occurrence of 5 → 1 CH…O hydrogen bond between the ith residue CH group and (i − 4)th residue CO with C…O ≤ 3.8 Å is studied, considering as potential donors the main‐chain Cα and the side‐chain carbon atoms Cβ, Cγ, Cδ and Cϵ. Similar analysis has been carried out for 4 → 1 CH…O hydrogen bonds, since the CH…O hydrogen bonds found in helices are predominantly of type 5 → 1 or 4 → 1. A total of 17,367 (9310 of type 5 → 1 and 8057 of type 4 → 1) CH…O hydrogen bonds are found to satisfy the selected criteria. The average stereochemical parameters for the data set suggest that the observed CH…O hydrogen bonds are attractive interactions. Our analysis reveals that the Cγ and Cβ hydrogen atom(s) are frequently involved in such hydrogen bonds. A marked preference is noticed for aliphatic β‐branched residue Ile to participate in 5 → 1 CH…O hydrogen bonds involving methylene Cγ 1 atom as donor in α‐helices. This may be an enthalpic compensation for the greater loss of side‐chain conformational entropy for β‐branched amino acids due to the constraint on side‐chain torsion angle, namely, χ1, when they occur in helices. The preference of amino acids for 4 → 1 CH…O hydrogen bonds is found to be more for Asp, Cys, and for aromatic residues Trp, Phe, and His. Interestingly, overall propensity for CH…O hydrogen bonds shows that a majority of the helix favoring residues such as Met, Glu, Arg, Lys, Leu, and Gln, which also have large side‐chains, prefer to be involved in such types of weak attractive interactions in helices. The amino acid side‐chains that participate in CH…O interactions are found to shield the acceptor carbonyl oxygen atom from the solvent. In addition, CH…O hydrogen bonds are present along with helix stabilizing salt bridges. A novel helix terminating interaction motif, X‐Gly with Gly at Ccap position having 5 → 1 CαH…O, and a chain reversal structural motif having 1 → 5 Cα‐H…O have been identified and discussed. Our analysis highlights that a multitude of local CH…O hydrogen bonds formed by a variety of amino acid side‐chains and Cα hydrogen atoms occur in helices and more so at the helix termini. It may be surmised that the main‐chain Cα and the side‐chain CH that participate in CH…O hydrogen bonds collectively augment the cohesive energy and thereby contribute together with the classical NH…O hydrogen bonds and other interactions to the overall stability of helix and therefore of proteins. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Effects of purified alginate sponge on the regeneration of chondrocytes: in vitro and in vivo

Regeneration science has been studied using tissue engineering techniques due to the self-renewal difficulties of damaged or degenerated cartilage. A scaffold with biodegradability and biocompatibility features plays a key role in developing cartilage tissue similar to human biological materials. Herein, we have fabricated three-dimensional sponge using purified alginate for the regeneration of chondrocytes cells and formation of cartilage. We demonstrated that the alginate purification can effectively minimize inflammatory reaction through reducing the content of mannuronic acid causing immune rejection. Cartilage regeneration research was performed using three-dimensional non-purified and purified alginate sponges synthesized by modified Korbutt method. In vitro cell viability and specific gene expression in the cartilage cells were investigated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and reverse transcriptase-polymerase chain reaction (RT-PCR) after seeding chondrocytes on the as-fabricated sponges. Specific extracellular matrix (ECM) of chondrocytes, sGAG, and the content of collagen were also measured. Histological staining was carried out after purified alginate sponge seeded with chondrocytes and was implanted in subcutaneous nude mouse followed by extraction. Compared to the non-purified ones, the purified alginate sponges showed positive effects on maintaining affinities and phenotype of chondrocytes. From these results, it can be suggested that the purified alginate sponges provide a promising platform for cartilage regeneration.
LLCPS and SISO: A TLS-based framework with RFID for NFC P2P retail transaction processing

The introduction of smartphones enabled with Near Field Communication (NFC) technology facilitates transformation of processes that involve manual intervention such as payment transaction processing in an automated manner. Although payment for transaction using NFC technology is not new, the possibility to use smartphones for payment either through stored payment information in the smartphone or in the cloud allows for seamless integration of associated processes. We consider advances in identification and communication technologies such as RFID (Radio Frequency IDentification) and smartphones as well as the ability to respond in real-time for automated checkout in a retail shopping environment with NFC-enabled smartphones. Using a recently proposed protocol (LLCPS) as an envelope for communication between the smartphone and the NFC reader, we develop a suite of authentication protocols (SISO) for secure payment processing in a retail store environment.
Activity Recognition Using Complex Network Analysis

In this paper, we perform complex network analysis on a connectivity dataset retrieved from a monitoring system in order to classify simple daily activities. The monitoring system is composed of a set of wearable sensing modules positioned on the subject's body and the connectivity data consists of the correlation between each pair of modules. A number of network measures are then computed followed by the application of statistical significance and feature selection methods. These methods were implemented for the purpose of reducing the total number of modules in the monitoring system required to provide accurate activity classification. The obtained results show that an overall accuracy of 84.6% for activity classification is achieved, using a random forest classifier, and when considering a monitoring system composed of only two modules positioned at the neck and thigh of the subject's body.
Enhancement of plasma wakefield generation and self-compression of femtosecond laser pulses by ionization gradients

As lasers become progressively higher in power, optical damage thresholds will become a limiting factor. Using the non-linear optics of plasma may be a way to circumvent these limits. In this paper, we report on simulations showing an enhancement to plasma wakefield self-compression of femtosecond laser pulses due to an ionization gradient at the leading edge of the pulse. By operating in a regime where wakefield generation is driven by moderately relativistic (∼1018 W cm−2) laser pulses and proper choice of gas species, the ionization front of the pulse can lead to a frequency shift that enhances the ponderomotive force and therefore both the wakefield generation and subsequent pulse compression.
Effects of Varying Rate of Signing on ASL Manual Signs and Nonmanual Markers

Spoken languages are characterized by flexible, multivariate prosodic systems. As a natural language, American Sign Language (ASL), and other sign languages (SLs), are also expected to be characterized in the same way. Artificially created signing systems for classroom use, such as signed English, serve as a contrast to natural sign languages. The present article explores the effects of changes in signing rate on signs, pauses, and, unlike previous studies, a variety of nonmanual markers. Rate was a main effect on the duration of signs, the number of pauses and pause duration, the duration of brow raises, the duration of licensed lowered brows, the number and duration of blinks, all of which decreased with increased signing rate. This indicates that signers produced their different signing rates without making dramatic changes in the number of signs, but instead by varying the sign duration, in accordance with previous observations (Grosjean, 1978, 1979). These results can be brought to bear on three different issues: (1) the difference between grammatical nonmanuals and non-grammatical nonmanuals; (2) the fact that nonmanuals in general are not just a modality effect; and (3) the use of some nonmanuals as pragmatically determined as opposed to overt morphophonological markers reflecting the semantic—syntax—pragmatic interfaces.
MOS Hardening Approaches for Low-Temperature Applications

Charge buildup in irradiated MOS devices is significantly more severe at low temperatures than at room temperature. Approaches for counteracting this problem are considered in this paper, including: (1) careful selection of the applied field; (2) ion implantation of the oxide; (3) use of a thin oxide. Experimental and analytical results are presented and it is demonstrated that the applied field dependence of flatband voltage shift in MOS capacitors irradiated at 77°K can be accounted for in terms of the field dependence of electron yield and the transport of holes at high fields. Analysis of ion implantation effects indicates that a significant improvement in radiation tolerance should be achievable by this method. A simultaneous consideration of the effects of oxide thickness and applied field on charge buildup in an unimplanted oxide suggests that reducing the thickness to ¿500 A° will largely eliminate low temperature problems in a steady-state ionizing radiation environment as long as the applied voltage is ¿ 10V.
Differential expression of a Clostridium acetobutylicum antisense RNA: implications for regulation of glutamine synthetase

The Clostridium acetobutylicum glutamine synthetase (GS) DNA region is characterized by a downstream promoter, P3, oriented toward the glnA gene, which controls the transcription of an RNA complementary to the start of the glnA mRNA. Expression of the predicted 43-base antisense RNA was demonstrated in C. acetobutylicum and Escherichia coli cells containing the cloned glnA DNA. Antisense RNA transcription from P3 was not regulated by nitrogen in E. coli cells, but the expression of antisense RNA was associated with decreased levels of GS activity. In C. acetobutylicum, GS activity and the transcription of glnA mRNA and antisense RNA were regulated by nitrogen. GS activity and glnA mRNA were repressed in cells grown in nitrogen-rich medium. Repression ratios for GS activity varied from 1.6 to 9.0, depending on the sampling time. The relative number of glnA transcripts was approximately 25% lower in cells grown for 72 h in nitrogen-rich medium than in cells grown in nitrogen-limiting medium. This finding contrasted with the expression of antisense RNA, which was repressed in nitrogen-limiting medium but induced in nitrogen-rich medium. The relative number of antisense RNA transcripts was increased approximately sixfold in cells grown in nitrogen-rich medium. There was a 1.6-fold excess of antisense RNA over glnA mRNA under conditions that repressed GS activity. Under conditions that induced GS activity, glnA mRNA transcripts exceeded antisense RNA transcripts by fivefold.
A dynamic programming solution for optimizing test delivery in multicore SOCs

We present a test-data delivery optimization algorithm for system-on-chip (SOC) designs with hundreds of cores, where a network-on-chip (NOC) is used as the interconnection fabric. The proposed algorithm is the first to co-optimize the number of access points, access-point locations, pin distribution to access points, and assignment of cores to access points for optimal test resource utilization. Test-time minimization for grid-based NOCs is modeled as an NOC partitioning problem and solved with dynamic programming in polynomial time. The proposed method yields high-quality results that are comparable to integer linear programming (ILP), but unlike ILP, it is scalable to large SOCs with many cores. We present results on synthetic NOC-based SOCs constructed using cores from the ITC'02 benchmark, and demonstrate the scalability of our approach for two SOCs of the future, one with nearly 1,000 cores and the other with 1,600 cores.
Fertility and pregnancy in the patient with inflammatory bowel disease

The majority of patients with inflammatory bowel disease (IBD) are affected during their peak reproductive years.1 While initial concerns focus on attaining a durable remission and avoiding the side effects of medications, once in remission the focus often shifts to the effect of disease and the medications used to treat it on fertility and the ability to conceive a healthy child. This paper summarises the existing literature on the effects of ulcerative colitis (UC) and Crohn’s disease (CD) and the medications used to treat it on fertility and pregnancy outcomes. Patients are naturally concerned about passing their disease on to their offspring. Unfortunately, family history is the strongest predictor for developing IBD. If one parent is affected, the risks of the offspring developing IBD are 2–13 times higher than in the general population.2,3 One study estimated that the risks of IBD in first degree relatives of probands with UC and CD were 1.6% and 5.2%, respectively, values that were even higher in the Jewish population.4 If both parents have IBD, the risk of their offspring developing IBD over their lifetime was estimated to be 36%. 5 Several studies suggest that breastfeeding may be protective against the development of IBD in the infant. In a meta-analysis of 17 studies, the eight highest quality studies showed a pooled odds ratio of 0.45 (0.26, 0.79) for CD and 0.56 (0.38, 0.81) for UC.6 However, these were not mothers who had IBD themselves. Infertility is defined as the diminished ability or the inability to conceive and have offspring. It is also defined in specific terms as failure to conceive after a year of regular intercourse without contraception. In general, women with CD appear to have similar fertility rates to the general population. Older referral centre studies estimated infertility rates …
On Discrimination in Procurement Auctions

With exogenous participation, strong bidders should be discriminated against weak bidders to maximize revenues (Myerson 1981). When participation is endogenous and the set of potential entrants is large, optimal discrimination if any takes a very different form. Without incumbents, there should be no discrimination even if entrants come from groups with different characteristics. With incumbents, those should be discriminated against entrants no matter how strong/weak they are even if some share of their surplus is internalized by the designer. The optimal reserve policy in standard auctions is also analyzed to shed light on situations in which discrimination is not permitted.
The unreasonable effectiveness of neural network approximation

Results concerning the approximation rates of neural networks are of particular interest to engineers. The results reported in the literature have "slow approximation rates" (of the order of 1//spl radic/m, where m is the number of parameters in the neural network). However many empirical studies report that neural network approximation is quite effective in practice. Here we give an explanation of this unreasonable effectiveness by proving the existence of a sequence of approximations that converge at a faster rate by using methods from number theory.
Sichtweisen und Anlageverhalten des österreichischen Fondsmanagements

Die Untersuchung basiert auf einer schriftlichen Befragung von Fondsmanagern in Osterreich. Sie offenbart deren positive Selbsteinschatzung hinsichtlich des beruflichen Erfolges, ohne dabei mit exzessiver Uberschatzung des eigenen Informationsstandes verbunden zu sein. Das Anlageverhalten der Fondsmanager weist grundsatzlich kaum Verzerrungen auf - weder exzessive Handelsaktivitat, noch einen Dispositionseffekt oder Verlustaversion. Allerdings ist festzustellen, dass insbesondere jungere, unerfahrene Fondsmanager zum Herdenverhalten neigen. In der Untersuchung offenbaren letztere aber keine hohere Risikoaversion, die im Allgemeinen mit Herdenverhalten assoziiert wird.
Tagging Funding Agencies and Grants in Scientific Articles using Sequential Learning Models

In this paper we present a solution for tagging funding bodies and grants in scientific articles using a combination of trained sequential learning models, namely conditional random fields (CRF), hidden markov models (HMM) and maximum entropy models (MaxEnt), on a benchmark set created in-house. We apply the trained models to address the BioASQ challenge 5c, which is a newly introduced task that aims to solve the problem of funding information extraction from scientific articles. Results in the dry-run data set of BioASQ task 5c show that the suggested approach can achieve a micro-recall of more than 85% in tagging both funding bodies and grants.
Effects of cigarette smoking upon clinical outcomes of assisted reproduction: a meta-analysis.

BACKGROUND The aim of this meta-analysis was to investigate whether any difference exists in success rate of clinical outcomes of assisted reproductive technologies (ART) between women who actively smoke cigarettes at the time of treatment and those who do not. METHODS An intensive computerized search was conducted on published literature from eight databases, using search terms related to smoking, assisted reproduction and outcome measures. Eligible studies compared outcomes of ART between cigarette smoking patients and a control group of non-smoking patients and reported on live birth rate per cycle, clinical pregnancy rate per cycle, ectopic pregnancy rate per pregnancy or spontaneous miscarriage rate per pregnancy, and 21 studies were included in the meta-analyses. Pooled odds ratios (OR) and 95% confidence intervals (CI) were calculated for the data, and statistical heterogeneity was tested for using chi(2) and I(2) values. A systematic review examined the effect of smoking upon fertilization rates across 17 studies. RESULTS Smoking patients demonstrated significantly lower odds of live birth per cycle (OR 0.54, 95% CI 0.30-0.99), significantly lower odds of clinical pregnancy per cycle (OR 0.56, 95% CI 0.43-0.73), significantly higher odds of spontaneous miscarriage (OR 2.65, 95% CI 1.33-5.30) and significantly higher odds of ectopic pregnancy (OR 15.69, 95% CI 2.87-85.76). A systematic literature review revealed that fertilization rates were not significantly different between smoking and non-smoking groups in most studies. CONCLUSIONS This meta-analysis provides compelling evidence for a significant negative effect of cigarette smoking upon clinical outcomes of ART and should be presented to infertility patients who smoke cigarettes in order to optimize success rates.
Association using modified Global Nearest Neighbor in the presence of bias

Global Nearest Neighbor (GNN) method has been widely implemented in multi-target multi-sensor tracking system, and has achieved a good tracking performance. However, the performance of this approach can be easily destroyed when the sensor biases are involved in the target observations, especially in the cluttered environment with false alarms and missed detections. In order to tackle this issue, this paper proposes a modified GNN method to associate observations and targets in the presence of the sensor bias. Compared with the traditional GNN method, the modified GNN method introduces the new concept of target pattern, and computes the similarity between observations using the feature vector which is constructed using the distance among observations. Simulations show that the modified GNN method has high association success rate, and is robust against the variation of the sensor bias, the number of targets, and the clutter density which the GNN method cannot handle well.
Refractive Error May Influence Mesopic Pupil Size

Purpose: To identify factors which affect mesopic pupil diameter in refractive surgery patients. Setting: This retrospective study was performed at the 1st Ophthalmology Clinic in Ankara Ataturk Training and Research Hospital, Ankara, Turkey. Methods: Medical records of 412 refractive surgery candidates who applied between 2006 and 2008 were reviewed. Detailed ophthalmological examination data were obtained from medical records. Pupil size measurements were performed with a COAS Ocular Wavefront analyzer in mesopic conditions. Relationship between mesopic pupil diameter and age, sex, spherical refractive error (D), magnitude of astigmatism (D), type of astigmatism, spherical equivalent, and average keratometry were analyzed by means of univariate and multivariate regression analyses. Results: Mean mesopic pupil diameter was 6.19 ± 0.88 mm. Mean pupil diameter (mean ± standard deviation) was 5.70 ± 1.01 in hypermetropia, 6.04 ± 0.79 mm in mixed astigmatism, and 6.33 ± 0.82 mm in myopia. The difference in mean mesopic pupil diameters between myopes and hypermetropes was statistically significant (p = 0.001). However, differences with regard to mean pupil diameters between myopes and mixed astigmatism (p = 0.660) and between hypermetropes and mixed astigmatism (p = 0.109) were not significant. Mean pupil diameter was 6.00 ± 0.99 mm in against the rule astigmatism, 5.96 ± 0.84 mm in oblique astigmatism, and 6.27 ± 0.84 mm in with the rule astigmatism. Mean mesopic pupil diameter in with the rule astigmatism group was higher than oblique astigmatism group. Spherical refractive error (r = -0.213, p = 0.001), cylindrical refractive error (0.197, p = 0.001), and age (r = −0.341, p = 0.001) showed correlation with pupil diameter. Conclusions: This study showed that age and magnitude of both spherical and cylindrical refractive error are the most determinative factors on mesopic pupil size.