Miracle-dz/UniFAR-FTUs huggingface dataset:
Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens

Clostridium perfringens is a commensal member of the human gut microbiome and an opportunistic pathogen whose genome encodes a suite of putative large, multi-modular carbohydrate-active enzymes that appears to play a role in the interaction of the bacterium with mucin-based carbohydrates. Among the most complex of these is an enzyme that contains a presumed catalytic module belonging to glycoside hydrolase family 31 (GH31). This large enzyme, which based on its possession of a GH31 module is a predicted α-glucosidase, contains a variety of non-catalytic ancillary modules, including three CBM32 modules that to date have not been characterized. NMR-based experiments demonstrated a preference of each module for galacto-configured sugars, including the ability of all three CBM32s to recognize the common mucin monosaccharide GalNAc. X-ray crystal structures of the CpGH31 CBM32s, both in apo form and bound to GalNAc, revealed the finely-tuned molecular strategies employed by these sequentially variable CBM32s in coordinating a common ligand. The data highlight that sequence similarities to previously characterized CBMs alone are insufficient for identifying the molecular mechanism of ligand binding by individual CBMs. Furthermore, the overlapping ligand binding profiles of the three CBMs provide a fail-safe mechanism for the recognition of GalNAc among the dense eukaryotic carbohydrate networks of the colonic mucosa. These findings expand our understanding of ligand targeting by large, multi-modular carbohydrate-active enzymes, and offer unique insights into of the expanding ligand-binding preferences and binding site topologies observed in CBM32s.
Development of a novel titration and off-gas analysis (TOGA) sensor for study of biological processes in wastewater treatment systems.

The development of the new TOGA (titration and off-gas analysis) sensor for the detailed study of biological processes in wastewater treatment systems is outlined. The main innovation of the sensor is the amalgamation of titrimetric and off-gas measurement techniques. The resulting measured signals are: hydrogen ion production rate (HPR), oxygen transfer rate (OTR), nitrogen transfer rate (NTR), and carbon dioxide transfer rate (CTR). While OTR and NTR are applicable to aerobic and anoxic conditions, respectively, HPR and CTR are useful signals under all of the conditions found in biological wastewater treatment systems, namely, aerobic, anoxic and anaerobic. The sensor is therefore a powerful tool for studying the key biological processes under all these conditions. A major benefit from the integration of the titrimetric and off-gas analysis methods is that the acid/base buffering systems, in particular the bicarbonate system, are properly accounted for. Experimental data resulting from the TOGA sensor in aerobic, anoxic, and anaerobic conditions demonstrates the strength of the new sensor. In the aerobic environment, carbon oxidation (using acetate as an example carbon source) and nitrification are studied. Both the carbon and ammonia removal rates measured by the sensor compare very well with those obtained from off-line chemical analysis. Further, the aerobic acetate removal process is examined at a fundamental level using the metabolic pathway and stoichiometry established in the literature, whereby the rate of formation of storage products is identified. Under anoxic conditions, the denitrification process is monitored and, again, the measured rate of nitrogen gas transfer (NTR) matches well with the removal of the oxidised nitrogen compounds (measured chemically). In the anaerobic environment, the enhanced biological phosphorus process was investigated. In this case, the measured sensor signals (HPR and CTR) resulting from acetate uptake were used to determine the ratio of the rates of carbon dioxide production by competing groups of microorganisms, which consequently is a measure of the activity of these organisms. The sensor involves the use of expensive equipment such as a mass spectrometer and requires special gases to operate, thus incurring significant capital and operational costs. This makes the sensor more an advanced laboratory tool than an on-line sensor.
Cementum and epithelial attachment response to the sulcular and periodontal ligament injection techniques.

This investigation studied the effect of the sulcular and periodontal ligament injection techniques on certain periodontal tissues. Eleven monkeys (Macaca nemistrina) were given injections of local anesthetic into the sulcular tissue or the periodontal ligament on the lingual side of maxillary molars. Contralateral teeth served as controls. After three months biopsies were taken and made into histologic sections. Of 6 teeth receiving a sulcular injection, 1 had a small area of cementum resorption. 0£ the 16 teeth which received a periodontal ligament injection, 2 had areas of cementum resorption and I showed an area of hypercementosis. No detrimental changes were found in the level of epithelial attachment. l/~. ~tandard(~ techniques" are used most often to achieve nerve block and infiltration anesthesia in dentistry. However, on occasion these techniques have proved to be either uncomfortable to the patient or have resulted in inadequate anesthesia. Consequently, practitioners have begun to modify existing techniques and develop new ones that meet their clinical needs. The sulcular and periodontal ligament injections are examples of such modifications. The sulcular injection technique is especially useful in the maxillary-posterior-lingual areas of the primary and mixed dentition. For example, it may be used in combination with a buccal infiltration before extraction, or when applying rubber dam clamps. In this technique the needle is inserted gently approximately 0.5-1.0 mm into the tissue at the bottom of the gingival sulcus and a small amount of solution is injected slowly (Figure 1). Clinically, the use of this method in pediatric dentistry causes no apparent damage to the periodontium. In addition, the procedure seems to be less painful and therefore better tolerated by patients than alternative injection techniques. Figure 1. Site of needle insertion when using the sulcular injection technique. 0.5-1 mm Figure 2. Site of needle insertion when using the periodontal ligament injection technique. The periodontal ligament (PDL) injection has been described by Mead, 1 Roberts and Sowray, 2 and Walton and Abbott.3 In this technique the needle is inserted into the PDL where the solution is injected (Figure 2). Favorable clinical experience using the sulcular and PDL injection techniques encourages further study. However, Mead1 and Roberts and Sowray2 expressed concern about possible detrimental effects from the intraPDL injection. These concerns apparently were based on clinical impressions.
Potentialities of Nonsmooth Optimization

In this paper, we show that higher-order optimality conditions can be obtain for arbitrary nonsmooth function. We introduce a new higher-order directional derivative and higher-order subdifferential of Hadamard type of a given proper extended real function. This derivative is consistent with the classical higher-order Fr\'echet directional derivative in the sense that both derivatives of the same order coincide if the last one exists. We obtain necessary and sufficient conditions of order $n$ ($n$ is a positive integer) for a local minimum and isolated local minimum of order $n$ in terms of these derivatives and subdifferentials. We do not require any restrictions on the function in our results. A special class $\mathcal F_n$ of functions is defined and optimality conditions for isolated local minimum of order $n$ for a function $f\in\mathcal F_n$ are derived. The derivative of order $n$ does not appear in these characterizations. We prove necessary and sufficient criteria such that every stationary point of order $n$ is a global minimizer. We compare our results with some previous ones.
Apples and Oranges: Detecting Least-Privilege Violators with Peer Group Analysis

Clustering software into peer groups based on its apparent functionality allows for simple, intuitive categorization of software that can, in particular, help identify which software uses comparatively more privilege than is necessary to implement its functionality. Such relative comparison can improve the security of a software ecosystem in a number of ways. For example, it can allow market operators to incentivize software developers to adhere to the principle of least privilege, e.g., by encouraging users to use alternative, less-privileged applications for any desired functionality. This paper introduces software peer group analysis, a novel technique to identify least privilege violation and rank software based on the severity of the violation. We show that peer group analysis is an effective tool for detecting and estimating the severity of least privilege violation. It provides intuitive, meaningful results, even across different definitions of peer groups and security-relevant privileges. Our evaluation is based on empirically applying our analysis to over a million software items, in two different online software markets, and on a validation of our assumptions in a medium-scale user study.
The Arecibo Legacy Fast ALFA Survey. II. Results of Precursor Observations

In preparation for the full Arecibo Legacy Fast ALFA (ALFALFA) extragalactic H I survey, precursor observations were carried out in 2004 August–September with the seven-beam Arecibo L-band Feed Array (ALFA) receiver system and the Wideband Arecibo Pulsar Processor spectral processors. While these observations were geared mainly at testing and debugging survey strategy, hardware, and software, approximately 48 hr of telescope time yielded science-quality data. The efficiency of system usage (allowing for minor malfunctions and the impact of radio-frequency interference) during that time was 75%. From those observations, an initial list of 730 tentative detections of varying degrees of reliability was extracted. Ninety-eight high signal-to-noise ratio candidates were deemed to be bona fide H I line detections. To test our ability to discriminate cosmic signals from radio-frequency interference and noise, 165 candidates ranging in reliability likelihood were reobserved with the single-beam L-band wide system at Arecibo in 2005 January–February. Of those, 41% were confirmed as real. We present the results of both the ALFA and the single-beam observations for the sample of 166 confirmed H I sources, as well as our assessment of their optical counterparts. Of the 166 sources, 62 coincided with previously known H I sources, while optical redshifts were available for an additional 18 galaxies; thus, 52% of the redshifts reported here were previously unknown. Of the 166 H I detections, 115 are identified with previously cataloged galaxies of either known or unknown redshift, leaving 51 objects identified for the first time. Because of the higher sensitivity of the Arecibo system, fewer than 10% of the 166 H I sources would have been detected by a HIPASS-like survey of the same region. Three of the objects have H I masses less than 107 M⊙. The full ALFALFA survey, which commenced in 2005 February, should detect more than 100 times as many objects of similarly low H I mass over the next 5 years.
The risk to relatives of patients with sporadic amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis is a neurodegenerative disease of motor neurons with a median survival of 2 years. Most patients have no family history of amyotrophic lateral sclerosis, but current understanding of such diseases suggests there should be an increased risk to relatives. Furthermore, it is a common question to be asked by patients and relatives in clinic. We therefore set out to determine the risk of amyotrophic lateral sclerosis to first degree relatives of patients with sporadic amyotrophic lateral sclerosis attending a specialist clinic. Case records of patients with sporadic amyotrophic lateral sclerosis seen at a tertiary referral centre over a 16-year period were reviewed, and pedigree structures extracted. All individuals who had originally presented with sporadic amyotrophic lateral sclerosis, but who subsequently had an affected first degree relative, were identified. Calculations were age-adjusted using clinic population demographics. Probands (n = 1502), full siblings (n = 1622) and full offspring (n = 1545) were identified. Eight of the siblings and 18 offspring had developed amyotrophic lateral sclerosis. The unadjusted risk of amyotrophic lateral sclerosis over the observation period was 0.5% for siblings and 1.0% for offspring. Age information was available for 476 siblings and 824 offspring. For this subset, the crude incidence of amyotrophic lateral sclerosis was 0.11% per year (0.05–0.21%) in siblings and 0.11% per year (0.06–0.19%) in offspring, and the clinic age-adjusted incidence rate was 0.12% per year (0.04–0.21%) in siblings. By age 85, siblings were found to have an 8-fold increased risk of amyotrophic lateral sclerosis, in comparison to the background population. In practice, this means the risk of remaining unaffected by age 85 dropped from 99.7% to 97.6%. Relatives of people with sporadic amyotrophic lateral sclerosis have a small but definite increased risk of being affected.
FYX-051: A Novel and Potent Hybrid-Type Inhibitor of Xanthine Oxidoreductase

4-[5-(Pyridin-4-yl)-1H-1,2,4-triazol-3-yl]pyridine-2-carbonitrile (FYX-051) is a potent inhibitor of bovine milk xanthine oxidoreductase (XOR). Steady-state kinetics study showed that it initially behaved as a competitive-type inhibitor with a Ki value of 5.7 × 10−9 M, then after a few minutes it formed a tight complex with XOR via a Mo-oxygen-carbon atom covalent linkage, as reported previously (Proc Natl Acad Sci USA 101:7931–7936, 2004). Thus, FYX-051 is a hybrid-type inhibitor exhibiting both structure- and mechanism-based inhibition. The FYX-051-XOR complex decomposed with a half-life of 20.4 h, but the enzyme activity did not fully recover. This was found to be caused by XOR-mediated conversion of FYX-051 to 4-[5-(2-hydroxypyridin-4-yl)-1H-1,2,4-triazol-3-yl]pyridine-2-carbonitrile (2-hydroxy-FYX-051), as well as formation of 6-hydroxy-4-[5-(2-hydroxypyridin-4-yl)-1H-1,2,4-triazol-3-yl]pyridine-2-carbonitrile (dihydroxy-FYX-051) and 4-[5-(2,6-dihydroxypyridin-4-yl)-1H-1,2,4-triazol-3-yl]-6-hydroxypyridine-2-carbonitrile (trihydroxy-FYX-051) during prolonged incubation for up to 72 h. A distinct charge-transfer band was observed concomitantly with the formation of the trihydroxy-FYX-051-XOR complex. Crystallographic analysis of the charge-transfer complex indicated that a Mo-nitrogen-carbon bond was formed between molybdenum of XOR and the nitrile group of trihydroxy-FYX-051. FYX-051 showed a potent and long-lasting hypouricemic effect in a rat model of potassium oxonate-induced hyperuricemia, and it seems to be a promising candidate for the clinical treatment of hyperuricemia.
Suppression effects of partner type on the alcohol-risky sex relationship in young Irish adults.

OBJECTIVE The present study examined the link between alcohol consumption and condom use, testing whether partner type suppresses the effects of alcohol consumption on condom use. This study also sought to determine whether the effects of alcohol on condom use during casual sex remain after adjusting for condom-use intentions and planning or preparatory behaviors, such as having a condom available. METHOD A retrospective, cross-sectional study design was used. A subset of participants aged 19-30 years from the national Irish Study of Sexual Health and Relationships were recontacted (n = 388). Telephone interviews regarding participants' most recent sexual event in their normal social environment (i.e., not on holidays) were conducted (n = 362). Partnership type was defined as "just met," "casual," or "steady. " Men comprised 51% of the sample. The mean age was 23.9 years. RESULTS Both alcohol consumption and condom use were more common in casual sexual events than steady sexual events. In addition, partnership type was found to suppress the effects of alcohol consumption on condom use, such that the relationship between alcohol consumption and condom use became significant and negative only after controlling for partner type. Furthermore, the negative effects of alcohol consumption on condom use during casual sex remained after adjusting for condom-use intentions and planning. CONCLUSIONS These findings illustrate the complexity of the relationship between alcohol consumption and condom use, highlighting the importance of contextual factors such as partner type. Furthermore, the effects of alcohol on condom use during casual sex cannot be explained by the fact that such events tend to be more spontaneous and less planned.
Pipelined implementation of adaptive multiple-antenna CDMA mobile receivers

Pipelined implementation of an adaptive direct-sequence code division multiple access (DS-CDMA) receiver is proposed when multiple antennas are utilized for mobile communications. Adaptive multiple-antenna receivers can provide insensitivity to the interfering powers and room for more users or require a smaller number of antennas than the matched filter solution. A number of approximation techniques are utilized to pipeline the adaptive algorithm used for the proposed multiple-antenna receiver. The resulting pipelined receiver requires minimal hardware increase and achieves a higher throughput or requires lower power as compared to the receiver using the serial algorithm. Simulation results illustrate the signal-to-interference ratio (SIR) versus the relative interfering power for different number of antennas and different levels of pipelining.
Breastfeeding and Reduced Risk of Sudden Infant Death Syndrome: A Meta-analysis

CONTEXT: Benefits of breastfeeding include lower risk of postneonatal mortality. However, it is unclear whether breastfeeding specifically lowers sudden infant death syndrome (SIDS) risk, because study results have been conflicting. OBJECTIVE: To perform a meta-analysis to measure the association between breastfeeding and SIDS. METHODS: We identified 288 studies with data on breastfeeding and SIDS through a Medline search (1966–2009), review articles, and meta-analyses. Twenty-four original case-control studies were identified that provided data on the relationship between breastfeeding and SIDS risk. Two teams of 2 reviewers evaluated study quality according to preset criteria; 6 studies were excluded, which resulted in 18 studies for analysis. Univariable and multivariable odds ratios were extracted. A summary odds ratio (SOR) was calculated for the odds ratios by using the fixed-effect and random-effect inverse-variance methods of meta-analysis. The Breslow-Day test for heterogeneity was performed. RESULTS: For infants who received any amount of breast milk for any duration, the univariable SOR was 0.40 (95% confidence interval [CI]: 0.35–0.44), and the multivariable SOR was 0.55 (95% CI: 0.44–0.69). For any breastfeeding at 2 months of age or older, the univariable SOR was 0.38 (95% CI: 0.27–0.54). The univariable SOR for exclusive breastfeeding of any duration was 0.27 (95% CI: 0.24–0.31). CONCLUSIONS: Breastfeeding is protective against SIDS, and this effect is stronger when breastfeeding is exclusive. The recommendation to breastfeed infants should be included with other SIDS risk-reduction messages to both reduce the risk of SIDS and promote breastfeeding for its many other infant and maternal health benefits.
Is Helicobacter Pylori Infection Associated with Asthma Risk? A Meta-Analysis Based on 770 Cases and 785 Controls

Objective: Helicobacter pylori (H. pylori) infection has been thought to play a critical role in disorders such as gastric and lung cancer. A number of studies have been devoted to the relationship between H. pylori infection and asthma risk, which have generated inconclusive results. In this study we aimed to derive a more precise estimation of the relationship. Methods: Meta-analyses evaluating the association of H. pylori infection and asthma risk were conducted and subgroup analyses on ethnicity and source of controls as well as CagA status were further conducted. Eligible studies were identified for the period up to Jul 2012. Results: A total of five case-control studies comprising 770 cases and 785 controls were lastly selected for analysis. The overall data failed to indicate a significant association of H. pylori infection and asthma risk (OR=1.01; 95%CI=0.82-1.24). Likewise, in the subgroup analysis regarding ethnicity, source of controls and CagA status, no associations could be observed. Conclusions: The pooled data failed to suggest a marked association between H. pylori infection and asthma risk. Future studies are needed to confirm this conclusion.
Chemical composition and evaluation of acute toxicological, antimicrobial and modulatory resistance of the extract of Murraya paniculata

Abstract Context: Murraya paniculata (Linn) JACK (Rutaceae) is used in traditional medicine in the treatment of diabetes, inflammation, and microbial disorders. Objective: This study determined the polyphenol composition and antimicrobial and acute toxicological activity of the hydroethanolic extract of M. paniculata leaves (EEMp). Materials and methods: Chemical composition was evaluated by the Folin–Ciocalteu and AlCl3 assays and by HPLC-DAD. Antibacterial and modulatory activity was determined by the microdilution method. Toxicity was assessed with a single dose of EEMp administered orally at doses of 2000 and 5000 mg/kg body weight/day in male and female Swiss mice. Results: Total phenolic content of the EEMp samples varied from 66.5 to 396.8 mg gallic acid equivalent/g of extract and flavonoid content varied from 0.3 to 31.1 mg quercetin equivalent/g of extract. The principal component identified by HPLC-DAD assay was ellagic acid. The results of oral acute toxicity showed no mortality, changes in hematological parameters, or CNS and ANS toxicities in rats. Biochemical analysis showed a significant increase in glucose and glutamic oxaloacetic transaminase activity and reduction in triglycerides and cholesterol for 5000 and 2000 mg/kg doses, respectively, when compared with the control group. Histopathological evaluation showed no significant microscopic changes. EEMp showed essentially no antimicrobial activity, but when aminoglycosides were combined with EEMp their MIC was reduced. Conclusions: Significant effects were observed in the acute toxicity assay, but they had no clinical relevance. The results suggest that M. paniculata could be used as a source of natural products with antibacterial resistance-modifying activity, with lower toxicity.
A Very Small Chaotic Neural Net

Previously we have shown that chaos can arise in networks of physically realistic neurons (C. Lourenco and A. Babloyantz, 1994), (C. Lourenco, 2006). Those networks contain a moderate to large number of units connected in a spatial arrangement providing instances of so-called cellular neural networks. It was proposed that the flexibility and wide range of behaviors of chaos could be of computational value, namely in spatiotemporal regimes and when coupled with a chaos control process, either in biological or artificial nets. Here we aim to find a minimal network of realistic neurons already featuring a chaotic regime. Such a small network can be computationally useful per se, or otherwise constitute the building block of larger networks with even richer dynamical regimes. Our investigation unveils the role of the interplay between a homoclinic tangency and the presence of delays in neural signal transmission in the creation of complex behavior.