Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and Biochemical Characterization of a Highly Stable Bacterial Laccase That Occurs as a Structural Component of theBacillus subtilis Endospore Coat*

The Bacillus subtilis endospore coat protein CotA shows laccase activity. By using comparative modeling techniques, we were able to derive a model for CotA based on the known x-ray structures of zucchini ascorbate oxidase and Cuprinus cereneus laccase. This model of CotA contains all the structural features of a laccase, including the reactive surface-exposed copper center (T1) and two buried copper centers (T2 and T3). Single amino acid substitutions in the CotA T1 copper center (H497A, or M502L) did not prevent assembly of the mutant proteins into the coat and did not alter the pattern of extractable coat polypeptides. However, in contrast to a wild type strain, both mutants produced unpigmented colonies and spores unable to oxidize syringaldazine (SGZ) and 2′2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS). The CotA protein was purified to homogeneity from an overproducingEscherichia coli strain. The purified CotA shows an absorbance and a EPR spectra typical of blue multicopper oxidases. Optimal enzymatic activity was found at ≤pH 3.0 and at pH 7.0 for ABTS or SGZ oxidation, respectively. The apparent K m values for ABTS and SGZ at 37 °C were of 106 ± 11 and 26 ± 2 μm, respectively, with correspondingk cat values of 16.8 ± 0.8 and 3.7 ± 0.1 s−1. Maximal enzyme activity was observed at 75 °C with ABTS as substrate. Remarkably, the coat-associated or the purified enzyme showed a half-life of inactivation at 80 °C of about 4 and 2 h, respectively, indicating that CotA is intrinsically highly thermostable.
An FPGA-based fast two-symbol processing architecture for JPEG 2000 arithmetic coding

In this paper, a field-programmable gate array (FPGA) based enhanced architecture of the arithmetic coder is proposed, which processes two symbols per clock cycle as compared to the conventional architecture that processes only one symbol per clock. The input to the arithmetic coder is from the bit-plane coder, which generates more than two context-decision pairs per clock cycle. But due to the slow processing speed of the arithmetic coder, the overall encoding becomes slow. Hence, to overcome this bottleneck and speed up the process, a two-symbol architecture is proposed which not only doubles the throughput, but also can be operated at frequencies greater than 100 MHz. This architecture achieves a throughput of 210 Msymbols/sec and the critical path is at 9.457 ns.
Sparse production but preferential incorporation of recently produced naïve T cells in the human peripheral pool

In mice, recent thymic emigrants (RTEs) make up a large part of the naïve T cell pool and have been suggested to be a distinct short-lived pool. In humans, however, the life span and number of RTEs are unknown. Although 2H2O labeling in young mice showed high thymic-dependent daily naïve T cell production, long term up- and down-labeling with 2H2O in human adults revealed a low daily production of naïve T cells. Using mathematical modeling, we estimated human naïve CD4 and CD8 T cell half-lives of 4.2 and 6.5 years, respectively, whereas memory CD4 and CD8 T cells had half-lives of 0.4 and 0.7 year. The estimated half-life of recently produced naïve T cells was much longer than these average half-lives. Thus, our data are incompatible with a substantial short-lived RTE population in human adults and suggest that the few naïve T cells that are newly produced are preferentially incorporated in the peripheral pool.
Isscc 2012 / Session 28 / Adaptive & Low-power Circuits / 28.1 28.1 a 4.5tb/s 3.4tb/s/w 64×64 Switch Fabric with Self-updating Least-recently-granted Priority and Quality-of-service Arbitration in 45nm Cmos

High-speed and low-power routers form the basic building blocks of on-die interconnect fabrics that are critical to overall throughput and energy efficiency of high performance systems [1,2]. Conventional routers use distinct logic blocks for routing data and handling arbitration [3,4]. At higher radices, connections between these blocks become a bottleneck, limiting router scalability and degrading performance. Recently, two switch topologies [5,6] merged the data-routing fabric with arbitration control, avoiding this bottleneck. However, [6] relies on centralized control for channel allocation, limiting performance, while [5] is restricted to a small set of fixed priorities, rendering input ports prone to starvation. In addition, ever larger CMPs will require continued increases in bandwidth over previous designs. To address these issues, we present a 64×64 single-stage swizzle-switch network (SSN) with 128b data buses (8192 total input/output wires). The SSN can connect any input to any output, including multicast. It has a peak measured throughput of 4.5Tb/s at 1.1V in 45nm SOI CMOS at 25°C. The SSN's key features are: 1) a single-cycle least-recently-granted (LRG) priority arbitration technique that reuses the already present input and output data buses and their drivers and sense amps; 2) an additional 4-level message-based priority arbitration for quality of service (QoS) with 2% logic and 3% wiring overhead; 3) a bidirectional bitline repeater that allows the router to scale to >8000 wires. These features result in a compact fabric (4.06mm 2) with throughput gain of 2.1× over [5] at 3.4Tb/s/W efficiency, which improves to 7.4Tb/s/W at 600mV. Conventional least-recently-granted LRG implementations use controllable delay elements to resolve conflicts [4]. Large routers require many such delay elements , incurring overhead and the probability of meta-stability failures. In contrast , SSN uses a fully static circuit technique that is completely embedded in the data routing fabric by reusing the data-routing bitlines as " priority lines " for arbitration. The LRG and QoS priorities and the switch configuration are all stored locally at each crosspoint using an encoding. Since the data routing fabric is routing limited, this additional logic imposes zero area overhead over a simple switch. Furthermore, as the arbitration logic reuses the data bitlines and periph-erals, arbitration has the same latency as data transfer and the two scale in tandem with the switch radix. The SSN is a matrix-type fabric (Fig. 28.1.1) with input buses running horizontally and output buses vertically. When data is routed, the input and output buses transfer …
The energy complexity of register files

Register files (RF) represent a substantial portion of the energy budget in modern processors, and are growing rapidly with the trend towards wider instruction issue. The actual access energy costs depend greatly on the register file circuitry used. This paper compares various RF circuitry techniques for their energy efficiencies, as a function of architectural parameters such as the number of registers and the number of ports. The port priority selection technique was found to be the most energy efficient. The dependence of register file access energy upon technology scaling is also studied. However, as this paper shows, it appears that none of these will be enough to prevent centralized register files from becoming the dominant power component of next-generation superscalar computers, and alternative methods for inter-instruction communication need to be developed. Split register file architecture is analyzed as a possible alternative.
DynaSoft: Dynamisch selbstorganisierende Softwaresysteme für Automobile

Software ist uber die Jahre zu dem wichtigsten Innovationstreiber in der Automobilindustrie geworden. Der Anteil der Software im Automobil steigt jahrlich aufgrund der Vorteile einer softwarebasierten Realisierung vieler Fahrzeugfunktionen rasant an. Die wachsende Anzahl, sowie die wachsende Vernetzung und Variantenvielfalt der Funktionen fuhrt zu einer immer schneller wachsenden Komplexitat automobiler Softwaresysteme. Um diese auch in Zukunft beherrschen zu konnen, sind grundsatzlich neue Entwicklungsansatze notwendig. Die Methoden der Selbstorganisation bilden hierfur eine vielversprechende Losung. Aus diesem Grund beschaftigt sich das Projekt DynaSoft mit der Umsetzung der Selbstorganisation in automobilen Softwaresystemen. Im Folgenden wird eine domanenspezifische Adaption der Selbstorganisation im Automobil vorgestellt und Begriffe der Selbstorganisation werden im automobilen Kontext definiert. Es werden Herausforderungen aufgezeigt, die sich bei der Umsetzung von Selbstorganisation im Automobil stellen. Schlieslich werden die im Projekt DynaSoft erarbeiteten Losungsansatze und identifizierte Problemstellungen bei der Einfuhrung selbstorganisierender Software in Fahrzeuge beschrieben.
Measurement of Visceral Fat: Should We Include Retroperitoneal Fat?

Objective Whether retroperitoneal fat should be included in the measurement of visceral fat remains controversial. We compared the relationships of fat areas in peritoneal, retroperitoneal, and subcutaneous compartments to metabolic syndrome, adipokines, and incident hypertension and diabetes. Methods We enrolled 432 adult participants (153 men and 279 women) in a community-based cohort study. Computed tomography at the umbilicus level was used to measure the fat areas. Results Retroperitoneal fat correlated significantly with metabolic syndrome (adjusted odds ratio (OR), 5.651, p<0.05) and the number of metabolic abnormalities (p<0.05). Retroperitoneal fat area was significantly associated with blood pressure, plasma glycemic indices, lipid profile, C-reactive protein, adiponectin (r = −0.244, P<0.05), and leptin (r = 0.323, p<0.05), but not plasma renin or aldosterone concentrations. During the 2.94±0.84 years of follow-up, 32 participants developed incident hypertension. Retroperitoneal fat area (hazard ration (HR) 1.62, p = 0.003) and peritoneal fat area (HR 1.62, p = 0.009), but not subcutaneous fat area (p = 0.14) were associated with incident hypertension. Neither retroperitoneal fat area, peritoneal fat area, nor subcutaneous fat areas was associated with incident diabetes after adjustment. Conclusions Retroperitoneal fat is similar to peritoneal fat, but differs from subcutaneous fat, in terms of its relationship with metabolic syndrome and incident hypertension. Retroperitoneal fat area should be included in the measurement of visceral fat for cardio-metabolic studies in human.
Fuzzy rules extraction using self-organising neural network and association rules

Fuzzy logic is becoming popular in dealing with data analysis problems that are normally handled by statistical approaches or ANNs. The major limitation is the difficulty in building the fuzzy rules from a given set of input-output data. This paper proposed a technique to extract fuzzy rules directly from input-output pairs. It uses a self-organising neural network and association rules to construct the fuzzy rule base. The self-organising neural network is first used to classify the output data by realising the probability distribution of the output space. Association rules are then used to find the relationships between the input space and the output classification, which are subsequently converted to fuzzy rules. This technique is fast and efficient. The results of an illustrative example show that the fuzzy rules extracted are promising and useful for domain experts.
Persistence of Th17/Tc17 Cell Expression upon Smoking Cessation in Mice with Cigarette Smoke-Induced Emphysema

Th17 and Tc17 cells may be involved in the pathogenesis of chronic obstructive pulmonary disease (COPD), a disease caused predominantly by cigarette smoking. Smoking cessation is the only intervention in the management of COPD. However, even after cessation, the airway inflammation may be present. In the current study, mice were exposed to room air or cigarette smoke for 24 weeks or 24 weeks followed by 12 weeks of cessation. Morphological changes were evaluated by mean linear intercepts (Lm) and destructive index (DI). The frequencies of CD8+IL-17+(Tc17) and CD4+IL-17+(Th17) cells, the mRNA levels of ROR gamma and IL-17, and the levels of IL-8, TNF-alpha, and IFN-gamma in lungs or bronchoalveolar lavage fluid of mice were assayed. Here we demonstrated that alveolar enlargement and destruction induced by cigarette smoke exposure were irreversible and that cigarette smokeenhanced these T-cell subsets, and related cytokines were not significantly reduced after smoking cessation. In addition, the frequencies of Th17 and Tc17 cells in lungs of smoke-exposed mice and cessation mice were positively correlated with emphysematous lesions. More important, the frequencies of Tc17 cells were much higher than Th17 cells, and there was a significantly positive correlation between Th17 and Tc17. These results suggested that Th17/Tc17 infiltration in lungs may play a critical role in sustaining lung inflammation in emphysema. Blocking the abnormally increased numbers of Tc17 and Th17 cells may be a reasonable therapeutic strategy for emphysema.
Lactobacillus paracasei normalizes muscle hypercontractility in a murine model of postinfective gut dysfunction.

BACKGROUND & AIMS The effects of probiotics on gut dysfunction in postinfective irritable bowel syndrome are unknown. We tested whether probiotics influence persistent muscle hypercontractility in mice after recovery from infection with Trichinella spiralis and analyzed the underlying mechanisms. METHODS Mice were gavaged with Lactobacillus paracasei, Lactobacillus johnsonii, Bifidobacterium longum, or Bifidobacterium lactis in spent culture medium from days 10 to 21 after infection. Additional mice received heat-inactivated Lactobacillus paracasei, Lactobacillus paracasei -free spent culture medium, or heat-inactivated Lactobacillus paracasei -free spent culture medium. Lactobacilli enumeration, immunohistochemistry, and cytokine detection (enzyme-linked immunosorbent assay) were performed. Mice were also treated with Lactobacillus paracasei or Lactobacillus paracasei -free spent culture medium from days 18 to 28 after infection. Contractility was measured on days 21 and 28 after infection. RESULTS Lactobacillus paracasei, but not Lactobacillus johnsonii, Bifidobacterium lactis, or Bifidobacterium longum, attenuated muscle hypercontractility. This was associated with a reduction in the Trichinella spiralis -associated T-helper 2 response and a reduction in transforming growth factor-beta1, cyclooxygenase-2, and prostaglandin E 2 levels in muscle. Attenuation of muscle hypercontractility by Lactobacillus paracasei -free spent culture medium was abolished after heat treatment. Improvement of muscle hypercontractility at day 28 after infection was also observed after the administration of Lactobacillus paracasei or Lactobacillus paracasei -free spent culture medium from day 18 after infection. CONCLUSIONS Probiotics show strain-dependent attenuation of muscle hypercontractility in an animal model of postinfective irritable bowel syndrome. This likely occurs via both a modulation of the immunologic response to infection and a direct effect of Lactobacillus paracasei or a heat-labile metabolite on postinfective muscle hypercontractility. Lactobacillus paracasei may be useful in the treatment of postinfective irritable bowel syndrome.
Identification of Rgg-Regulated Exoproteins ofStreptococcus pyogenes

ABSTRACT Streptococcus pyogenes secretes many proteins that influence host-pathogen interactions. Despite their importance, relatively little is known about the regulation of these proteins. Thergg gene (also known as ropB) is required for the expression of streptococcal erythrogenic toxin B (SPE B), an extracellular cysteine protease that contributes to virulence. Proteomics was used to determine if rgg regulates the expression of additional exoproteins. Exponential- and stationary-phase culture supernatant proteins made by S. pyogenes NZ131rgg and NZ131 speB were separated by two-dimensional electrophoresis. Differences were identified in supernatant proteins from both exponential- and stationary-phase cultures, although considerably more differences were detected among stationary-phase supernatant proteins. Forty-two proteins were identified by peptide fingerprinting with matrix-assisted laser desorption mass spectrometry. Mitogenic factor, DNA entry nuclease (open reading frame [ORF 226]), and ORF 953, which has no known function, were more abundant in the culture supernatants of thergg mutant compared to the speB mutant. ClpB, lysozyme, and autolysin were detected in the culture supernatant of thespeB mutant but not the rgg mutant. To determine if Rgg affected protein expression at the transcriptional level, real-time (TaqMan) reverse transcription (RT)-PCR was used to quantitate Rgg-regulated transcripts from NZ131 wild-type andspeB and rgg mutant strains. The results obtained with RT-PCR correlated with the proteomic data. We conclude that Rgg regulates the transcription of several genes expressed primarily during the stationary phase of growth.
Accelerating Markov Chain Monte Carlo Simulation by Differential Evolution with Self-Adaptive Randomized Subspace Sampling

Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.
Acceleration Axis Selection in Biometric Technique Based on Gesture Recognition

This article proposes a biometric technique based on gesture recognition performed directly in a mobile device embedding an accelerometer. As time consumption is an essential requirement, this article aims to discover the most distinctive acceleration axis information in order to find the best strategy considering EER and consumed time. Best EER result of 2.5% has been obtained when the information of accelerations on each of the three axis is analyzed. When reducing the information inspected to only two or one acceleration axis signals, EER values are 2.98% and 4.34% respectively. Preprocessing various acceleration signals by calculating their magnitude outcomes with higher EER values. All this work has been developed from a database of 34 individuals who have performed their identifying gestures, and three falsifiers who have attempted to forge each original in-air signatures from studying video records.
Learned Cardiac Control with Heart Rate Biofeedback Transfers to Emotional Reactions

Emotions involve subjective feelings, action tendencies and physiological reactions. Earlier findings suggest that biofeedback might provide a way to regulate the physiological components of emotions. The present study investigates if learned heart rate regulation with biofeedback transfers to emotional situations without biofeedback. First, participants learned to decrease heart rate using biofeedback. Then, inter-individual differences in the acquired skill predicted how well they could decrease heart rate reactivity when later exposed to negative arousing pictures without biofeedback. These findings suggest that (i) short lasting biofeedback training improves heart rate regulation and (ii) the learned ability transfers to emotion challenging situations without biofeedback. Thus, heart rate biofeedback training may enable regulation of bodily aspects of emotion also when feedback is not available.
Obliterative Versus Reconstructive Prolapse Repair for Women Older than 70: Is There an Optimal Approach?

Objectives This study aimed to evaluate outcomes among women 70 years and older who underwent obliterative compared with reconstructive procedures for pelvic organ prolapse. Methods This was a retrospective cohort study of patients 70 years and older who underwent surgical prolapse repair at our institution from January 2004 through June 2010. Only patients with at least 4 weeks of follow-up were included. Patient characteristics and relevant pre, intra, and postoperative information were abstracted from medical records. Severity of postoperative complications was classified using the Dindo surgical classification system. Results We analyzed 143 (97.3%) patients. Fifty-four (37.8%) women underwent an obliterative procedure, whereas 89 (62.2%) underwent a reconstructive procedure. Twenty-eight (31.5%) women who had a reconstructive surgery met our criteria for recurrent prolapse compared with only 5 (9.3%) women in the obliterative group (P = 0.002). The incidence of intraoperative complication was 4.9%, and the incidence of any postoperative complication was 62.9%. Similar proportions of women who underwent each type of procedure experienced a postoperative complication. However, the severity of the complications differed between the groups (P = 0.02). In particular, 16.9% of women who had a reconstructive procedure experienced a grade III complication according to the Dindo scale compared with 13.0% of women who had an obliterative procedure. Conclusions The majority of women 70 years and older do not have high-grade complications after pelvic organ prolapse repair, but women who undergo reconstructive procedures are more likely to experience high-grade complications and recurrent prolapse compared with women who undergo obliterative procedures.