Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving the alkalophilic performances of the Xyl1 xylanase from Streptomyces sp. S38: Structural comparison and mutational analysis

Endo‐β‐1,4‐xylanases of the family 11 glycosyl‐hydrolases are catalytically active over a wide range of pH. Xyl1 from Streptomyces sp. S38 belongs to this family, and its optimum pH for enzymatic activity is 6. Xyn11 from Bacillus agaradhaerens and XylJ from Bacillus sp. 41M‐1 share 85% sequence identity and have been described as highly alkalophilic enzymes. In an attempt to better understand the alkalophilic adaptation of xylanases, the three‐dimensional structures of Xyn11 and Xyl1 were compared. This comparison highlighted an increased number of salt‐bridges and the presence of more charged residues in the catalytic cleft as well as an eight‐residue‐longer loop in the alkalophilic xylanase Xyn11. Some of these charges were introduced in the structure of Xyl1 by site‐directed mutagenesis with substitutions Y16D, S18E, G50R, N92D, A135Q, E139K, and Y186E. Furthermore, the eight additional loop residues of Xyn11 were introduced in the homologous loop of Xyl1. In addition, the coding sequence of the XylJ catalytic domain was synthesized by recursive PCR, expressed in a Streptomyces host, purified, and characterized together with the Xyl1 mutants. The Y186E substitution inactivated Xyl1, but the activity was restored when this mutation was combined with the G50R or S18E substitutions. Interestingly, the E139K mutation raised the optimum pH of Xyl1 from 6 to 7.5 but had no effect when combined with the N92D substitution. Modeling studies identified the possible formation of an interaction between the introduced lysine and the substrate, which could be eliminated by the formation of a putative salt‐bridge in the N92D/E139K mutant.
Fluorescence Microlymphography

Microneedles, 0.2 mm o.d. , were connected to a microsyringe and mounted on a micromanipulator. Under microscopic control, 0.01 ml of a 25% solution of FITC-labeled dextran-40 or dextran- 150 were injected into the subepidermis at the big toe near the nailfold or in the medial ankle region. Fluorescence intravital microscopy revealed a network of lymphatic microvessels. The comparison with recent anatomic studies reveals that the reticular network visualized by FITC-dextran corresponds to the network in the stratum papillare. In 20 healthy subjects lymphatic capillaries were detected in a restricted area on the lateral aspect of the big toe. In 10 patients with primary lymphedema, the dye expanded to almost the entire dorsal skin surface of the big toe. In two cases, enlarged and tortuous microvessels of pathologic shape were observed.Fluorescence microlymphography is a simple and nearly atraumatic approach for depicting the intravital anatomy of human skin lymphatic capillaries.
The changes of climate may threat the production of Grana Padano cheese: past, recent and future scenarios

Abstract Climate and animal agriculture are interrelated processes and related foods may be threatened through changes in temperature, rainfall and extreme weather events. The present study was aimed to investigate the climate trend over the production area of Grana Padano (GP) cheese. The area is in North of Italy, covers a total land of 46,000 km2 and it is highly suited for agricultural and livestock productions. Past (1971–2000), recent (2001–2010) and future (2020–2050) climate scenarios were considered and compared. The analysis showed positive anomalies both for minimum and maximum temperatures and a decrease of precipitation for recent and future climate. The Gaussen-Bagnouls classification pointed out a change from humid to semi-humid climate during summer months. These data suggest a warming trend and increasing risk of summer aridity over the production area of GP cheese. The analysis of temperature-humidity index (THI), from past throughout the future scenario, highlighted an increased risk of heat stress for dairy cows. The worst THI condition was predicted for July of the future scenario when milk loss may reach a level of 7 kg/cow/day. The changes in climate may threat the potential to produce GP cheese, indirectly by the negative effect of precipitation deficit on crops yield for cows feeding, directly by the increase of heat stress-related milk loss. These findings may be of help to animate the debate on climate change-related impacts on regional food systems and support policymakers in developing adaptation strategies for the production system of GP cheese. Highlights Climate is changing in the north Italy. Warming and aridity trend may threat the production of Grana Padano cheese. Adaptation measures are required.
Use of Fourier-Transform Infrared Spectroscopy for Typing of Candidaalbicans Strains Isolated in Intensive Care Units

ABSTRACT Comparative studies of Candidaalbicans strains are essential for proving cross-infections in epidemiological investigations. Typing of C. albicans strains is mainly based on genotypic methods. Fourier-transform infrared (FTIR) spectroscopy is described in this study as a novel phenotypic approach to the typing of C. albicans. The first step in the approach was the standardization of sample preparation (culture conditions and sampling parameters) and acquisition and classification parameters (spectral acquisition, spectral window selection, classification algorithm, and heterogeneity threshold). The second step consisted of validating the established parameters with a set of 79 strains of C. albicans isolated over 4 months from nine patients hospitalized in two intensive care units. Strains were isolated from multiple anatomical sites with repeated sampling. FTIR spectroscopy results were compared to randomly amplified polymorphic DNA (RAPD) results; this analysis showed that the amplification patterns of strains isolated from a given patient were identical and that different patients had different profiles. FTIR spectroscopy data were analyzed by hierarchical clustering performed with the second-derivative spectra. This classification revealed nine groups, one per patient. Only one spectrum out of 79 was misclassified by the FTIR spectroscopy method. RAPD and FTIR spectroscopy results were in good agreement, showing that, when nosocomial candidiasis transmission is suspected and urgent information is needed, this technique may be useful as a quick identification tool to give solid clues before confirmation by a genotypic method.
Low interobserver reliability of radiographic signs predicting healing disturbance in displaced intracapsular fracture of the femoral neck

We determined the interobserver agreement of 3 radiographic signs previously shown to predict a disturbance in healing of femoral neck fractures. 6 orthopedic surgeons evaluated 32 radiographs for the presence of comminution of the femoral calcar, varus displacement in excess of 30 degrees and a small head fragment. They also classified the radiographs with Garden's method and determined the presence or absence of displacement. The kappa values were 0.2 for comminution of the calcar, 0.5 for varus displacement and 0.4 for a small head fragment. In the Garden classification, the kappa value was 0.4, increasing to 0.6 when divided into Garden 1-2 and 3-4. When the fracture was classified as displaced or undisplaced, the kappa value was 0.5. The strength of agreement of signs predicting a disturbance in healing was thus shown to be poor to moderate.
Isolation and initial characterization of a series of Chlamydia trachomatis isolates selected for hydroxyurea resistance by a stepwise procedure

Chlamydiae are obligate intracellular bacteria that are dependent on eukaryotic host cells for ribonucleoside triphosphates but not deoxyribonucleotide triphosphates. Ribonucleotide reductase is the only enzyme known to catalyze the direct conversion of a ribonucleotide to a deoxyribonucleotide. Hydroxyurea inhibits ribonucleotide reductase by inactivating the tyrosine free radical present in the small subunit of the enzyme. In this report, we show that Chlamydia trachomatis growth is inhibited by hydroxyurea in both wild-type mouse L cells and hydroxyurea-resistant mouse L cells. Hydroxyurea was used as a selective agent in culture to isolate, by a stepwise procedure, a series of C. trachomatis isolates with increasing levels of resistance to the cytotoxic effects of the drug. One of the drug-resistant C. trachomatis isolates (L2HR-10.0) was studied in more detail. L2HR-10.0 retained its drug resistance phenotype even after passage in the absence of hydroxyurea for 10 growth cycles. In addition, L2HR-10.0 was cross resistant to guanazole, another inhibitor of ribonucleotide reductase. Results obtained from hydroxyurea inhibition studies using various host cell-parasite combinations indicated that inhibition of host cell and C. trachomatis DNA synthesis by hydroxyurea can occur but need not occur simultaneously. Crude extract prepared from highly purified C. trachomatis reticulate bodies was capable of reducing CDP to dCDP. The CDP reductase activity was not inhibited by monoclonal antibodies to the large and small subunits of mammalian ribonucleotide reductase, suggesting that the activity is chlamydia specific. The CDP reductase activity was inhibited by hydroxyurea. Crude extract prepared from drug-resistant L2HR-10.0 reticulate bodies contained an elevation in ribonucleotide reductase activity. In total, our results indicate that C. trachomatis obtains the precursors for DNA synthesis as ribonucleotides with subsequent conversion to deoxyribonucleotides catalyzed by a chlamydia-specific ribonucleotide reductase.
Cytoplasmic nucleophosmin in acute myelogenous leukemia with a normal karyotype.

BACKGROUND Nucleophosmin (NPM), a nucleocytoplasmic shuttling protein with prominent nucleolar localization, regulates the ARF-p53 tumor-suppressor pathway. Translocations involving the NPM gene cause cytoplasmic dislocation of the NPM protein. METHODS We used immunohistochemical methods to study the subcellular localization of NPM in bone marrow-biopsy specimens from 591 patients with primary acute myelogenous leukemia (AML). We then correlated the presence of cytoplasmic NPM with clinical and biologic features of the disease. RESULTS Cytoplasmic NPM was detected in 208 (35.2 percent) of the 591 specimens from patients with primary AML but not in 135 secondary AML specimens or in 980 hematopoietic or extrahematopoietic neoplasms other than AML. It was associated with a wide spectrum of morphologic subtypes of the disease, a normal karyotype, and responsiveness to induction chemotherapy, but not with recurrent genetic abnormalities. There was a high frequency of FLT3 internal tandem duplications and absence of CD34 and CD133 in AML specimens with a normal karyotype and cytoplasmic dislocation of NPM, but not in those in which the protein was restricted to the nucleus. AML specimens with cytoplasmic NPM carried mutations of the NPM gene that were predicted to alter the protein at its C-terminal; this mutant gene caused cytoplasmic localization of NPM in transfected cells. CONCLUSIONS Cytoplasmic NPM is a characteristic feature of a large subgroup of patients with AML who have a normal karyotype, NPM gene mutations, and responsiveness to induction chemotherapy.
Characterizing Postoperative Pain Management Data by Cluster Analysis

PCA (Patient Controlled Analgesia) is a delivery system for pain medication that makes effective and flexible pain treatments possible by allowing patients to adjust the dosage of analgesics themselves. Unlike previous research on patient controlled analgesia, this study explores patient demand behavior over time. We applied clustering methods to disclose demand patterns among patients over the first 24h of analgesic medication after surgery. We first identified three demand patterns from patient controlled analgesia request log files. We then considered demographic, biomedical, and surgery-related data to evaluate the influence of demand pattern on analgesic requirements. We recovered several associations that concurred with previous findings, and discovered several new correlations
Comparison between the Doppler flowmetry and the free flow of dog's internal thoracic artery with and without use norepinephrine.

OBJECTIVE This work aims to study comparatively the free flow and the Doppler flowmetry of the internal thoracic artery in anesthetized dogs, with and without continuous intravenous administration of norepinephrine. METHODS The sample was made up of ten mongrel dogs, which dissected the left and right internal thoracic arteries and evaluated your stream; first, by Doppler flowmetry and then by free flow. The mean arterial pressure and the diameter of the arteries at the beginning of the procedure were registered. The workflow checks by two methods occurred in three times: time zero, 10 and 25 minutes. After the first check in time zero, the continuous infusion of norepinephrine in the right atrium; other checks were made in the same way that the first time, to 10 and 25 minutes, in the same arteries and by two methods, each one in his artery, noting the results, as well as the corresponding average blood pressure. RESULTS The results of the scan of the stream, between Doppler flowmetry and free flow, there were similar; being the first, zero times, ten and twenty-five minutes, respectively, 183, 230.1 and 237 ml/min compared to seconds, 168.6, 226.8 and 226.4 ml/min (P = 0.285). The mean arterial pressures of three times and the average diameter of the arteries, showed no statistically significant differences between the methods, so did not influence on the comparison of the results. CONCLUSION The evaluations, both from Doppler flowmetry and free flow, were similar in three times checked.
Machine Translation Using Overlapping Alignments and SampleRank

We present a conditional-random-field approach to discriminatively-trained phrase-based machine translation in which training and decoding are both cast in a sampling framework and are implemented uniformly in a new probabilistic programming language for factor graphs. In traditional phrase-based translation, decoding infers both a "Viterbi" alignment and the target sentence. In contrast, in our approach, a rich overlapping-phrase alignment is produced by a fast deterministic method, while probabilistic decoding infers only the target sentence, which is then able to leverage arbitrary features of the entire source sentence, target sentence and alignment. By using SampleRank for learning we could in principle efficiently estimate hundreds of thousands of parameters. Test-time decoding is done by MCMC sampling with annealing. To demonstrate the potential of our approach we show preliminary experiments leveraging alignments that may contain overlapping bi-phrases.
Accelerated Turnover of Metaphyseal Trabecular Bone in Mice Overexpressing Cathepsin K

This study is based on a hypothesis that overexpression of an osteoclast enzyme, cathepsin K, causes an imbalance in bone remodeling toward bone loss. The hypothesis was tested in transgenic (TG) mice harboring additional copies of the murine cathepsin K gene (Ctsk) identifiable by a silent mutation engineered into the construct. For this study, three TG mouse lines harboring 3‐25 copies of the transgene were selected. Tissue specificity of transgene expression was determined by Northern analysis, which revealed up to 6‐fold increases in the levels of cathepsin K messenger RNA (mRNA) in calvarial and long bone samples of the three TG lines. No changes were seen in the mRNA levels of other osteoclast enzymes, indicating that the increase in cathepsin K mRNA was not a reflection of activation of all osteoclast enzymes. Immunohistochemistry confirmed that cathepsin K expression in the TG mice was confined to osteoclasts and chondroclasts. Histomorphometry revealed a significantly decreased trabecular bone volume (BV), but, surprisingly, also a marked increase in the number of osteoblasts, the rate of bone turnover, and the amount of mineralizing surface (MS). However, monitoring of bone density in the proximal tibias of the TG mice with peripheral quantitative computed tomography (pQCT) failed to reveal statistically significant changes in bone density. Similarly, no statistically significant alterations were observed in biomechanical testing at the age of 7 months. The increases in parameters of bone formation triggered by increased cathepsin K expression is an example of the tight coupling of bone resorption and formation during the bone‐remodeling cycle.
ABSENCE OF FAST-MOVING IRON IN AN INTERMEDIATE TYPE Ia SUPERNOVA BETWEEN NORMAL AND SUPER-CHANDRASEKHAR

In this paper, we report observations of a peculiar SN Ia iPTF13asv (a.k.a., SN2013cv) from the onset of the explosion to months after its peak. The early-phase spectra of iPTF13asv show an absence of iron absorption, indicating that synthesized iron elements are confined to low-velocity regions of the ejecta, which, in turn, implies a stratified ejecta structure along the line of sight. Our analysis of iPTF13asv’s light curves and spectra shows that it is an intermediate case between normal and super-Chandrasekhar events. On the one hand, its light curve shape (B-band ) and overall spectral features resemble those of normal SNe Ia. On the other hand, its large peak optical and UV luminosity ( , ) and its low but almost constant Si ii velocities of about 10,000 km s−1 are similar to those in super-Chandrasekhar events, and its persistent carbon signatures in the spectra are weaker than those seen commonly in super-Chandrasekhar events. We estimate a 56Ni mass of and a total ejecta mass of . The large ejecta mass of iPTF13asv and its stratified ejecta structure together seemingly favor a double-degenerate origin.
Computers in Industry

Smart-Product Service Systems (S-PSS) emerge as a novel strategy to integrate smart products with advanced digital capabilities and their related e-services to satisfy user’s needs in highly context-dependent environments. S-PSS has the potential to generate a transition towards more economically, ecologically and socially sustainable practices and business models due to its adaptive capacities. However, being able to exploit the digital capabilities of smart products and their services is still limited in design and even more to improve the user experience. For this reason, this study will focus on the Context-awareness capability that has been defined by multiple scholars as one of the most relevant properties that defines the smartness of a product. Following a systematic literature review approach, this work makes the following contributions:
Magnetic resonance imaging of the upper airway in patients with quadriplegia and obstructive sleep apnea

The aim of this study was to investigate upper airway anatomy in quadriplegics with obstructive sleep apnea. Fifty subjects were recruited from three hospitals in Australia: people with quadriplegia due to spinal cord injury and obstructive sleep apnea (n = 11), able‐bodied people with obstructive sleep apnea (n = 18), and healthy, able‐bodied controls (n = 19). All underwent 3‐Tesla magnetic resonance imaging of their upper airway. A subgroup (n = 34) received a topical vasoconstrictor, phenylephrine and post‐phenylephrine magnetic resonance imaging. Mixed‐model analysis indicated no significant differences in total airway lumen volume between the three groups (P = 0.086). Spinal cord injury–obstructive sleep apnea subjects had a significantly larger volume of soft palate (P = 0.020) and retroglossal lateral pharyngeal walls (P = 0.043) than able‐bodied controls. Able‐bodied–obstructive sleep apnea subjects had a smaller mandible volume than spinal cord injury–obstructive sleep apnea subjects and able‐bodied control subjects (P = 0.036). No differences were seen in airway length between groups when controlling for height (P = 0.055). There was a marginal increase in velopharyngeal volume across groups post‐phenylephrine (P = 0.050), and post hoc testing indicated the difference was confined to the able‐bodied–obstructive sleep apnea group (P < 0.001). No other upper airway structures showed significant changes with phenylephrine administration. In conclusion, people with obstructive sleep apnea and quadriplegia do not have a structurally smaller airway than able‐bodied subjects. They did, however, have greater volumes of soft palate and lateral pharyngeal walls, possibly due to greater neck fat deposition. The acute response to upper airway topical vasoconstriction was not enhanced in those with obstructive sleep apnea and quadriplegia. Changes in upper airway anatomy likely contribute to the high incidence in obstructive sleep apnea in quadriplegic subjects.
Reporting randomized controlled trials. An experiment and a call for responses from readers.

The best information concerning therapeutic interventions comes from randomized controlled trials (RCTs). The validity of an RCT depends on the correct performance of a large number of essential steps. Unless all these steps are accurately accounted for and described, critical clinicians cannot know what actually took place, cannot judge whether the conclusions drawn by the authors are justified, and cannot judge whether their patients are likely to be helped or harmed by the intervention. See also p 1015. The object of an RCT is to produce an unbiased estimate of the effect of a therapy, a goal thwarted if allocation of patients is not random. In the February 1, 1995, issue of JAMA , we published a study of controlled trials by Schulz and colleagues. 1 These authors evaluated 250 controlled trials from 33 meta-analyses and found that when the treatment allocation was inadequately concealed from study participants and investigators, when
The Scottish Parliament and e-democracy

Purpose – To describe the initiatives of the Scottish Parliament in the field of e‐democracy and assess the prospects for future developments.Design/methodology/approach – Analysis and review.Findings – The Scottish Parliament has always seen the internet as one of the major mechanisms for engaging Scottish citizens in the Parliament's business and activities. Its most successful initiatives have been the e‐petitioning system, the webcasting of proceedings, the discussion forums and the MSP video diaries.Research limitations/implications – Relevant to parliaments and other representative institutions.Practical implications – Simple implementable tools are described that have been shown to be effective.Originality/value – Few parliaments have been able to put theory into practice in a short time. Applicable to other small parliaments with limited resources wishing to enhance democratic participation by electronic means.
THE INFORMATION CARRIED IN TONAL CONTRASTS IN P HOM ∗

Corpus measurements of tonal ambiguity in written Phom as a function of word size, N-gram context, and frequency are reported. A significant inverse relation between the number of syllables in a word and the tonal contrast size was found, while frequency of the preceding context was shown to be positively correlated with the size of the contrast comprising the ambiguity. N-gram context was also inversely related to the probability of disambiguation, but measures of relative entropy revealed this effect to be nonlinear; i.e. gains in information at the bigram were significantly greater than further gains in the trigram context.