Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature Regulation of the Hemin Storage (Hms+) Phenotype of Yersinia pestis Is Posttranscriptional

ABSTRACT In Yersinia pestis, the Congo red (and hemin) binding that is characteristic of the Hms+ phenotype occurs at temperatures up to 34°C but not at higher temperatures. Manifestation of the Hms+ phenotype requires at least five proteins (HmsH, -F, -R, -S, and -T) that are organized into two separate operons: hmsHFRS and hmsT. HmsH and HmsF are outer membrane proteins, while HmsR, HmsS, and HmsT are predicted to be inner membrane proteins. We have used transcriptional reporter constructs, RNA dot blots, and Western blots to examine the expression of hms operons and proteins. Our studies indicate that transcription from the hmsHFRS and hmsT promoters is not regulated by the iron status of the cells, growth temperature, or any of the Hms proteins. In addition, the level of mRNA for both operons is not significantly affected by growth temperature. However, protein levels of HmsH, HmsR, and HmsT in cells grown at 37°C are very low compared to those in cells grown at 26°C, while the amounts of HmsF and HmsS show only a moderate reduction at the higher growth temperature. Neither the Pla protease nor a putative endopeptidase (Y2360) encoded upstream of hmsH is essential for temperature regulation of the Hms+ phenotype. However, HmsT at 37°C is sensitive to degradation by Lon and/or ClpPX. Thus, the stability of HmsH, HmsR, and HmsT proteins likely plays a role in temperature regulation of the Hms+ phenotype of Y. pestis.
Analysis, Design, and Iterative Decoding of Double Serially Concatenated Codes with Interleavers

A double serially concatenated code with two interleavers consists of the cascade of an outer encoder, an interleaver permuting the outer codeword bits, a middle encoder, another interleaver permuting the middle codeword bits, and an inner encoder whose input words are the permuted middle codewords. The construction can be generalized to h cascaded encoders separated by h-1 interleavers, where h>3. We obtain upper bounds to the average maximum likelihood bit-error probability of double serially concatenated block and convolutional coding schemes. Then, we derive design guidelines for the outer, middle, and inner codes that maximize the interleaver gain and the asymptotic slope of the error probability curves. Finally, we propose a low-complexity iterative decoding algorithm. Comparisons with parallel concatenated convolutional codes, known as "turbo codes", and with the proposed serially concatenated convolutional codes are also presented, showing that in some cases, the new schemes offer better performance.
Secondary Ion Mass Spectroscopy Study of Oxygen‐18 Tracer Diffusion in 2/1‐Mullite Single Crystals

Oxygen 18O tracer diffusion in Czochralski-grown mullite single crystals is investigated along [010] and [001]. Oxygen diffusion coefficients range between ∼5 × 10−20 m2/s (1250°C) and ∼9 × 10−18 m2/s (1525°C). The data does not show any significant anisotropy. The values of the activation enthalpy (4.5 eV) and of the activation entropy ((3.4 ± 1.6)kB, where kB is the Boltzmann constant) suggest that the atomic transport occurs via thermally activated vacancies.
A Survey of Radio Resource Management for Spectrum Aggregation in LTE-Advanced

In order to satisfy the requirements of future IMT-Advanced mobile systems, the concept of spectrum aggregation is introduced by 3GPP in its new LTE-Advanced (LTE Rel. 10) standards. While spectrum aggregation allows aggregation of carrier components (CCs) dispersed within and across different bands (intra/inter-band) as well as combination of CCs having different bandwidths, spectrum aggregation is expected to provide a powerful boost to the user throughput in LTE-Advanced (LTE-A). However, introduction of spectrum aggregation or carrier aggregation (CA) as referred to in LTE Rel. 10, has required some changes from the baseline LTE Rel. 8 although each CC in LTE-A remains backward compatible with LTE Rel. 8. This article provides a review of spectrum aggregation techniques, followed by requirements on radio resource management (RRM) functionality in support of CA. On-going research on the different RRM aspects and algorithms to support CA in LTE-Advanced are surveyed. Technical challenges for future research on aggregation in LTE-Advanced systems are also outlined.
The Hydroxypyruvate-Reducing System in Arabidopsis: Multiple Enzymes for the Same End1[W]

Hydroxypyruvate (HP) is an intermediate of the photorespiratory pathway that originates in the oxygenase activity of the key enzyme of photosynthetic CO2 assimilation, Rubisco. In course of this high-throughput pathway, a peroxisomal transamination reaction converts serine to HP, most of which is subsequently reduced to glycerate by the NADH-dependent peroxisomal enzyme HP reductase (HPR1). In addition, a NADPH-dependent cytosolic HPR2 provides an efficient extraperoxisomal bypass. The combined deletion of these two enzymes, however, does not result in a fully lethal photorespiratory phenotype, indicating even more redundancy in the photorespiratory HP-into-glycerate conversion. Here, we report on a third enzyme, HPR3 (At1g12550), in Arabidopsis (Arabidopsis thaliana), which also reduces HP to glycerate and shows even more activity with glyoxylate, a more upstream intermediate of the photorespiratory cycle. The deletion of HPR3 by T-DNA insertion mutagenesis results in slightly altered leaf concentrations of the photorespiratory intermediates HP, glycerate, and glycine, indicating a disrupted photorespiratory flux, but not in visible alteration of the phenotype. On the other hand, the combined deletion of HPR1, HPR2, and HPR3 causes increased growth retardation, decreased photochemical efficiency, and reduced oxygen-dependent gas exchange in comparison with the hpr1xhpr2 double mutant. Since in silico analysis and proteomic studies from other groups indicate targeting of HPR3 to the chloroplast, this enzyme could provide a compensatory bypass for the reduction of HP and glyoxylate within this compartment.
Large Quantum Gravity Effects: Unforeseen Limitations of the Classical Theory.

3-dimensional gravity coupled to Maxwell (or Klein-Gordon) fields is exactly soluble under the assumption of axi-symmetry. The solution is used to probe several quantum gravity issues. In particular, it is shown that the quantum fluctuations in the geometry are large unless the number and frequency of photons satisfy the inequality $\N(\hbar G\omega)^2 << 1$. Thus, even when there is a single photon of Planckian frequency, the quantum uncertainties in the metric are significant. Results hold also for a sector of the 4-dimensional theory (consisting of Einstein Rosen gravitational waves).
Abnormal body composition phenotypes in Vietnamese women with early rheumatoid arthritis.

OBJECTIVES To characterize body composition phenotypes using a dual-energy X-ray absorptiometry (DXA) method and to explore factors potentially contributing to alterations in body composition in Vietnamese women with early RA. METHODS A total of 105 women with early RA (disease duration ≤ 3 years) and 105 age-matched healthy women underwent physical examination, total and regional lean mass (LM) and fat mass (FM) with DXA. The 28-joint DAS (DAS-28) and disability using HAQ score, nutrition, physical activity and medications were recorded. RESULTS Means of weight and BMI were similar in RA patients and controls, but means of total body and trunk FM in RA patients were higher: 19.1 vs 16.9 kg (P = 0.007) and 10.1 vs 8.1 kg (P = 0.01), respectively, and appendicular LM was lower: 12.9 vs 14.1 kg (P = 0.02). The proportion of unhealthy body composition phenotypes (sarcopenia, overfat and sarcopenic obesity) in RA patients was higher (P < 0.001) than in controls. DAS-28 score was positively correlated with total FM and fat distribution ratio, and HAQ score was inversely correlated with appendicular LM. These body composition changes were associated with RF seropositivity, HAQ and DAS-28 scores. CONCLUSIONS Women with early RA had a significantly higher proportion of unhealthy body composition phenotypes, higher total and truncal FM and lower appendicular LM than controls. Disease activity and disability scores were associated with unhealthy body composition. These findings suggest that clinicians should encourage muscle strengthening and fat loss in RA patients to reduce their disability.
Iterative Convex Refinement for Sparse Recovery

In this letter, we address sparse signal recovery in a Bayesian framework where sparsity is enforced on reconstruction coefficients via probabilistic priors. In particular, we focus on the setup of Yen who employ a variant of spike and slab prior to encourage sparsity. The optimization problem resulting from this model has broad applicability in recovery and regression problems and is known to be a hard non-convex problem whose existing solutions involve simplifying assumptions and/or relaxations. We propose an approach called Iterative Convex Refinement (ICR) that aims to solve the aforementioned optimization problem directly allowing for greater generality in the sparse structure. Essentially, ICR solves a sequence of convex optimization problems such that sequence of solutions converges to a sub-optimal solution of the original hard optimization problem. We propose two versions of our algorithm: a. ) an unconstrained version, and b. ) with a non-negativity constraint on sparse coefficients, which may be required in some real-world problems. Experimental validation is performed on both synthetic data and for a real-world image recovery problem, which illustrates merits of ICR over state of the art alternatives.
A Radiologic Survey of Various Configurations of the Lumbar Spine

This paper reports an investigation to determine whether or not human spine configurations can be categorized into types by which one could predict the possibility of disablement at one specific level more than another. Configurations of the lumbar spine, the shape of the lower two lumbar discs, the anterior and posterior heights of discs, the sizes of the transverse processes of L4–5, the presence or absence of rudimentary ribs, and the presence of transitional vertebrae were studied in roentgenograms of 554 subjects. They concluded that the probable criteria for development of L4–5 degeneration were 1) high intercrestal line passing through the upper half of L4, 2) long transverse process on L5, 3) rudimentary rib, and 4) transitional vertebra. Criteria for development of L5-S1 degeneration were 1) intercrestal line passing through the body of L5, 2) short transverse process on L5, 3) no rudimentary rib, 4) no transitional vertebrae. A high intercrestal line and long transverse process probably act as antitorsional devices protecting the L5-S1 disc; hence the likelihood of degeneration at L4–5 is increased.
Texture image segmentation by hierarchical modeling

The Texture Fragmentation and Reconstruction (TFR) algorithm has been recently proposed for the unsupervised hierarchical segmentation of textures. It is based on a hierarchical image model, where textures are characterized in terms of their spatial interaction properties, modeled by means of a set of Markov chains, each one associated with a major spatial direction. The TFR algorithm fits the image to the hierarchical model by means of a split-and-merge procedure where the first step (fragmentation) aims at extracting the elementary texture states, which are progressively merged in the second step (reconstruction), so as to obtain a hierarchical nested segmentation. Although TFR results are usually very good, it has been sometimes observed a bias towards the undersegmentation for complex images. Here, we analyze this phenomenon and propose the use of an improved fragmentation step, where would-be elementary states are ranked based on a suitable measure of their reliability and possibly purged. Experimental results validate the effectiveness of the new algorithm.
1 Do-It-Yourself Haptics , Part II : Interaction Design

This article is the second of a two-part series intended to be an introduction to haptic interfaces, their construction and application design. Haptic interactions employ mechanical, programmed physical devices which can be used for humancomputer communication via the sense of touch. In Part I of this series, we focused on the devices themselves: the classes of hardware schemes currently available or envisioned, the software components which drive them, and specific examples which can be built “on the kitchen table”. Here in Part II, we broach a topic which is coming into its own: between the vision of a particular utility that haptic feedback theoretically should enable, and the hardware capable of delivering the required sensations, is the problem of designing the interaction in a usable way.
Nitazoxanide for the treatment of Clostridium difficile colitis.

BACKGROUND Clostridium difficile colitis has increased in incidence and severity, and treatment failure with metronidazole therapy has increasingly been documented. It is uncertain whether treatment with vancomycin is more effective than treatment with metronidazole, but concern over the emergence of vancomycin resistance has motivated the search for alternative therapy. Nitazoxanide, a nitrothiazolide, blocks anaerobic metabolism of eukaryocyes and effectively treats intestinal infestation due to Cryptosporidium or Giardia species. At low concentrations, this compound inhibits C. difficile in vitro. METHODS We designed a prospective, randomized, double-blind study to compare nitazoxanide to metronidazole in treating hospitalized patients with C. difficile colitis. RESULTS Thirty-four patients received metronidazole at a dosage of 250 mg 4 times per day for 10 days, 40 patients received nitazoxanide at a dosage of 500 mg 2 times per day for 7 days, and 36 patients received nitazoxanide at a dosage of 500 mg 2 times per day for 10 days. After 7 days of treatment, 28 (82.4%) of 34 patients had responded to metronidazole therapy, compared with 68 (89.5%) of 76 who had received nitazoxanide therapy (difference, 7.1%; 95% confidence interval, -7.1% to 25.5%). Thirty-one days after beginning treatment, sustained responses were observed in 19 (57.6%) of 33 patients who had received metronidazole therapy for 10 days, compared with 25 (65.8%) of 38 who had received nitazoxanide for 7 days and 26 (74.3%) of 35 who had received nitazoxanide for 10 days (P = .34). CONCLUSION Nitazoxanide is at least as effective as metronidazole in treating C. difficile colitis.
Critical current density of Nb3Sn wires after irradiation with 65MeV and 24GeV protons

Industrial Nb3Sn wires with Ti and Ta additives (RRP process) and with Ta additives (PIT process) with a diameter of 1 mm have been irradiated at room temperature with protons of 65 MeV and of 24 GeV at various fluences up to 1×1021 p/m2. A steady increase of Jc vs. fluence was observed for all the wires up to the highest fluence. The observed increase of Jc at 4.2K in all wires was quite similar in spite of the very different proton energies. With increasing fluence. the radiation induced pinning force was found to increase. the enhancement Jc/Jco after 5.04×1020 p/m2 reaching 1.4 for Ta and 1.8 for Ti alloyed wires at 10T. The present results were quantitatively analysed by assuming a radiation induced point pinning mechanism in addition to grain boundary pinning. The results are compared with those of an ongoing neutron irradiation study undertaken on the same Nb3Sn wires in collaboration with the Atominstitut Vienna. Proton irradiation was found to produce considerably higher damage than neutron irradiation.
Template‐based recognition of protein fold within the midnight and twilight zones of protein sequence similarity

Most homologous pairs of proteins have no significant sequence similarity to each other and are not identified by direct sequence comparison or profile‐based strategies. However, multiple sequence alignments of low similarity homologues typically reveal a limited number of positions that are well conserved despite diversity of function. It may be inferred that conservation at most of these positions is the result of the importance of the contribution of these amino acids to the folding and stability of the protein. As such, these amino acids and their relative positions may define a structural signature. We demonstrate that extraction of this fold template provides the basis for the sequence database to be searched for patterns consistent with the fold, enabling identification of homologs that are not recognized by global sequence analysis.
Maximal Inhibition of SERCA2 Ca2+ Affinity by Phospholamban in Transgenic Hearts Overexpressing a Non-phosphorylatable Form of Phospholamban*

Phospholamban is a phosphoprotein in the cardiac sarcoplasmic reticulum (SR) which regulates the apparent Ca2+ affinity of the SR Ca2+-ATPase (SERCA2). To determine the levels of phospholamban which are associated with maximal inhibition of SERCA2, several lines of transgenic mice were generated which expressed increasing levels of a non-phosphorylatable form of phospholamban (S16A,T17A) specifically in the heart. This mutant form of phospholamban was chosen to prevent phosphorylation as a compensatory mechanism in vivo. Quantitative immunoblotting revealed increased phospholamban protein levels of 1.8-, 2.6-, 3.7-, and 4.7-fold in transgenic hearts compared with wild types. There were no changes in the expression levels of SERCA2, calsequestrin, calreticulin, and ryanodine receptor. Assessment of SR Ca2+ uptake in hearts of transgenic mice indicated increases in the inhibition of the affinity of SERCA2 for Ca2+ with increased phospholamban expression. Maximal inhibition was obtained at phospholamban expression levels of 2.6-fold or higher. Transgenic hearts with functional saturation in phospholamban:SERCA2 (≥2.6:1) exhibited increases in β-myosin heavy chain expression, associated with cardiac hypertrophy. These findings demonstrate that overexpression of a non-phosphorylatable form of phospholamban in transgenic mouse hearts resulted in saturation of the functional phospholamban:SERCA2 ratio at 2.6:1 and suggest that approximately 40% of the SR Ca2+pumps are functionally regulated by phospholamban in vivo.
Respiratory infection.

The RCN Learning Zone is a FREE online service to help RCN members with their continuing professional development and professional portfolio management. The RCN Learning Zone can be found at www.rcn. org.uk/members/learningzone.php This practice profile is based on NS681 Gould D (2013) Healthcareassociated respiratory tract infection. Nursing Standard. 27, 25, 50-56. Reading the CPD article has improved my knowledge of the care and management of patients at increased risk of acquiring healthcare-associated infections, which are highest among patients in intensive care units. Patients who are acutely ill are at increased risk of acquiring healthcare-associated respiratory tract infections – especially if the patient is mechanically ventilated or prescribed antibiotics, which result in the suppression of normal flora of the oropharynx and their replacement by gram-negative opportunistic bacteria. An inflammatory response is initiated when microorganisms access the lower respiratory tract, causing the mucous membranes to swell and pus to collect, thereby impeding gaseous exchange. Tracheobronchitis and pneumonia are the most common healthcare-associated respiratory tract infections. Pneumonia is an infection of the lung involving the alveoli and small airways, and when it develops in a patient more than 48 hours after hospital admission, it is diagnosed as healthcare-associated pneumonia. In tracheobronchitis, infection involves the trachea and bronchi, but not the alveoli. These lower respiratory tract infections are common in post-operative patients. For example, in patients who are mechanically ventilated, pneumonia may develop within 48 hours of intubation with an endotracheal tube. Poor practices among healthcare professionals can result in patients acquiring healthcare-associated respiratory tract infections. Inadequate hand hygiene, a hospital environment that is contaminated with pathogens from other patients or patients re-contaminating themselves are examples. It is important to adhere to hand hygiene policies to prevent cross-infection and ensure that the equipment used is managed appropriately, using autoclaving, for example. During two placements on surgical wards, I was involved in the care of post-operative patients. The patients were monitored on fluid balance charts to encourage rehydration, and fluids were administered intravenously if necessary until the patients were fully awake and could drink sufficient fluid orally to maintain hydration. Staff also administered analgesics for pain relief and positioned patients to promote diaphragm and intercostal muscle activity, hence improving ventilation.
JASPAR: an open-access database for eukaryotic transcription factor binding profiles

The analysis of regulatory regions in genome sequences is strongly based on the detection of potential transcription factor binding sites. The preferred models for representation of transcription factor binding specificity have been termed position-specific scoring matrices. JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes. The profiles were derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind transcription factors. The database is complemented by a web interface for browsing, searching and subset selection, an online sequence analysis utility and a suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. JASPAR is available at http://jaspar. cgb.ki. se.
Window Size Impact in Human Activity Recognition

Signal segmentation is a crucial stage in the activity recognition process; however, this has been rarely and vaguely characterized so far. Windowing approaches are normally used for segmentation, but no clear consensus exists on which window size should be preferably employed. In fact, most designs normally rely on figures used in previous works, but with no strict studies that support them. Intuitively, decreasing the window size allows for a faster activity detection, as well as reduced resources and energy needs. On the contrary, large data windows are normally considered for the recognition of complex activities. In this work, we present an extensive study to fairly characterize the windowing procedure, to determine its impact within the activity recognition process and to help clarify some of the habitual assumptions made during the recognition system design. To that end, some of the most widely used activity recognition procedures are evaluated for a wide range of window sizes and activities. From the evaluation, the interval 1–2 s proves to provide the best trade-off between recognition speed and accuracy. The study, specifically intended for on-body activity recognition systems, further provides designers with a set of guidelines devised to facilitate the system definition and configuration according to the particular application requirements and target activities.