Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression and Molecular Characterization of a Xylanase from Chicken Cecum Metagenome

A xylanase gene xynAMG1 with a 1,116-bp open reading frame, encoding an endo-β-1,4-xylanase, was cloned from a chicken cecum metagenome. The translated XynAMG1 protein consisted of 372 amino acids including a putative signal peptide of 23 amino acids. The calculated molecular mass of the mature XynAMG1 was 40,013 Da, with a theoretical pI value of 5.76. The amino acid sequence of XynAMG1 showed 59% identity to endo-β-1,4-xylanase from Prevotella bryantii and Prevotella ruminicola and 58% identity to that from Prevotella copri. XynAMG1 has two conserved motifs, DVVNE and TEXD, containing two active site glutamates and an invariant asparagine, characteristic of GH10 family xylanase. The xynAMG1 gene without signal peptide sequence was cloned and fused with thioredoxin protein (Trx.Tag) in pET-32a plasmid and overexpressed in Escherichia coli Tuner™(DE3)pLysS. The purified mature XynAMG1 was highly salt-tolerant and stable and displayed higher than 96% of its catalytic activity in the reaction containing 1 to 4 M NaCl. It was only slightly affected by common organic solvents added in aqueous solution to up to 5 M. This chicken cecum metagenome-derived xylanase has potential applications in animal feed additives and industrial enzymatic processes requiring exposure to high concentrations of salt and organic solvents.
Characterization of Plant Carotenoid Cyclases as Members of the Flavoprotein Family Functioning with No Net Redox Change1[W][OA]

The later steps of carotenoid biosynthesis involve the formation of cyclic carotenoids. The reaction is catalyzed by lycopene β-cyclase (LCY-B), which converts lycopene into β-carotene, and by capsanthin-capsorubin synthase (CCS), which is mainly dedicated to the synthesis of κ-cyclic carotenoids (capsanthin and capsorubin) but also has LCY-B activity. Although the peptide sequences of plant LCY-Bs and CCS contain a putative dinucleotide-binding motif, it is believed that these two carotenoid cyclases proceed via protic activation and stabilization of resulting carbocation intermediates. Using pepper (Capsicum annuum) CCS as a prototypic carotenoid cyclase, we show that the monomeric protein contains one noncovalently bound flavin adenine dinucleotide (FAD) that is essential for enzyme activity only in the presence of NADPH, which functions as the FAD reductant. The reaction proceeds without transfer of hydrogen from the dinucleotide cofactors to β-carotene or capsanthin. Using site-directed mutagenesis, amino acids potentially involved in the protic activation were identified. Substitutions of alanine, lysine, and arginine for glutamate-295 in the conserved 293-FLEET-297 motif of pepper CCS or LCY-B abolish the formation of β-carotene and κ-cyclic carotenoids. We also found that mutations of the equivalent glutamate-196 located in the 194-LIEDT-198 domain of structurally divergent bacterial LCY-B abolish the formation of β-carotene. The data herein reveal plant carotenoid cyclases to be novel enzymes that combine characteristics of non-metal-assisted terpene cyclases with those attributes typically found in flavoenzymes that catalyze reactions, with no net redox, such as type 2 isopentenyl diphosphate isomerase. Thus, FAD in its reduced form could be implicated in the stabilization of the carbocation intermediate.
Transmission of prion diseases by blood transfusion.

Attempts to detect infectivity in the blood of humans and animals affected with transmissible spongiform encephalopathies (TSEs or prion diseases) have often been inconclusive because of the limitations of cross-species bioassays and the small volumes of blood that can be injected by the intracerebral route. A model has been developed for the experimental study of TSE transmission by blood transfusion using sheep experimentally infected with bovine spongiform encephalopathy (BSE) or natural scrapie as donors and susceptible scrapie-free sheep as recipients. Donors and recipients of the same species greatly increase the sensitivity of the bioassay and in sheep large volumes of blood can be injected by the intravenous (i.v.) route. Transmission of BSE to a single animal using this approach was reported recently. This study confirms this result with a second transmission of BSE and four new cases of transmission of natural scrapie. Positive transmissions occurred with blood taken at pre-clinical and clinical stages of infection. Initial studies indicate that following such infection by the i.v. route, deposition of the abnormal prion protein isoform, PrP(Sc), in peripheral tissues may be much more limited than is seen following oral infection. These results confirm the risks of TSE infection via blood products and suggest that the measures taken to restrict the use of blood in the UK have been fully justified.
A Ba 2-resistant , acid-sensitive K conductance in Na-absorbing H 441 human airway epithelial cells

Inglis SK, Brown SG, Constable MJ, McTavish N, Olver RE, Wilson SM. A Ba -resistant, acid-sensitive K conductance in Na -absorbing H441 human airway epithelial cells. Am J Physiol Lung Cell Mol Physiol 292: L1304–L1312, 2007. First published February 2, 2007; doi:10.1152/ajplung.00424. 2006. —By analysis of whole cell membrane currents in Na -absorbing H441 human airway epithelial cells, we have identified a K conductance (GK) resistant to Ba but sensitive to bupivacaine or extracellular acidification. In polarized H441 monolayers, we have demonstrated that bupivacaine, lidocaine, and quinidine inhibit basolateral membrane K current (IBl) whereas Ba has only a weak inhibitory effect. IBl was also inhibited by basolateral acidification, and, although subsequent addition of bupivacaine caused a further fall in IBl, acidification had no effect after bupivacaine, demonstrating that cells grown under these conditions express at least two different bupivacaine-sensitive K channels, only one of which is acid sensitive. Basolateral acidification also inhibited short-circuit current (ISC), and basolateral bupivacaine, lidocaine, quinidine, and Ba inhibited ISC at concentrations similar to those needed to inhibit IBl, suggesting that the K channels underlying IBl are part of the absorptive mechanism. Analyses using RT-PCR showed that mRNA encoding several two-pore domain K (K2P) channels was detected in cells grown under standard conditions (TWIK-1, TREK-1, TASK-2, TWIK-2, KCNK-7, TASK-3, TREK-2, THIK-1, and TALK-2). We therefore suggest that K2P channels underlie GK in unstimulated cells and so maintain the driving force for Na absorption. Since this ion transport process is vital to lung function, K2P channels thus play an important but previously undocumented role in pulmonary physiology.
A novel physiologic model for the study of abdominal compartment syndrome (ACS).

BACKGROUND : Current abdominal compartment syndrome (ACS) models rely on intraperitoneal instillation of fluid, air, and other space-occupying substances. Although this allows for the study of the effects of increased abdominal pressure, it poorly mimics its pathogenesis. We have developed the first reported large animal model of ACS incorporating hemorrhagic shock/resuscitation. METHODS : Hemorrhagic shock was induced and maintained (1 hour) in 12 Yorkshire swine by bleeding to a mean arterial pressure (MAP) of 50 mm Hg. The collected blood plus two additional volumes of crystalloid was then reinfused. Mesenteric venous hypertension was induced by tightening a previously placed portal vein snare in a nonocclusive manner to mimic the effects of abdominal packing. Crystalloids were infused to maintain MAP. Hemodynamic measurements, abdominal pressure, peak inspiratory pressures, urine output, and blood chemistries were measured sequentially. Animals were studied for 36 hours after decompression. RESULTS : ACS (intra-abdominal pressure of > or =20 mm Hg with new organ dysfunction) developed in all animals. There were significant increases in peak inspiratory pressure, central venous pressure, and pulmonary artery pressure and decreases in MAP upon development of ACS. Urine output was significantly decreased before decompression. Mean blood lactate decreased and base excess increased significantly after decompression. CONCLUSIONS : We have created the first reported physiologic animal ACS model incorporating hemorrhagic shock/resuscitation and the effects of damage control surgery.
Cluster-Based Point Set Saliency

We propose a cluster-based approach to point set saliency detection, a challenge since point sets lack topological information. A point set is first decomposed into small clusters, using fuzzy clustering. We evaluate cluster uniqueness and spatial distribution of each cluster and combine these values into a cluster saliency function. Finally, the probabilities of points belonging to each cluster are used to assign a saliency to each point. Our approach detects fine-scale salient features and uninteresting regions consistently have lower saliency values. We evaluate the proposed saliency model by testing our saliency-based keypoint detection against a 3D interest point detection benchmark. The evaluation shows that our method achieves a good balance between false positive and false negative error rates, without using any topological information.
Energy requirements for racing endurance sled dogs*

Endurance sled dogs have unique dietary energy requirements. At present, there is disparity in the literature regarding energy expenditure and thus energy requirements of these dogs. We sought to further elucidate energy requirements for endurance sled dogs under field conditions. Three sled dog teams completing the 2011 Yukon Quest volunteered to provide diet history. Nutritional content was evaluated and a mock meal was analysed for each team. Race data were obtained from www.yukonquest. com. Dogs were weighed at the start of the race in Whitehorse Yukon (WH), a mid-way checkpoint in Dawson Yukon (DS) and at the finish in Fairbanks Alaska. Data are average value per dog or per dog per d. Linear regression compared average weight loss to average kcal/dog consumed daily. Diets and feeding regimes were similar for all three teams. The average daily energy intake and nutrient content was similar for all diets. During leg one (WH to DS), team 1 gained weight overall, whereas the other two teams experienced weight loss. Linear regression revealed 37 638 kJ/dog/d (8995 kcal/dog/d) was required for weight maintenance. During leg two (DS to Fairbanks Alaska), average weights decreased for all three teams. The extrapolated kcal requirement was approximately 57 734 kJ/dog/d (13 799 kcal/dog/d). The carbohydrate contents of these diets also suggest that presumed fat intake for endurance sled dogs may be slightly less than previously thought. Finally, these data support the concept that dietary energy requirements vary substantially with additional variables such as load pulled, terrain and ambient temperature.
Combination Therapy with Antiangiogenic Treatment and Photodynamic Therapy for the Nude Mouse Bearing U87 Glioblastoma

The objective of this study was to evaluate the effects of combination therapy with photodynamic therapy (PDT) and a novel antiangiogenic regimen using monoclonal antibodies against both vascular endothelial growth factor receptors (VEGFR)‐1 (MF1) and VEGFR‐2 (DC101) on intracranial glioblastoma xenografts in nude mice. Nude mice bearing intracerebral U87 glioblastoma were treated with PDT and the antiangiogenic regimen (MF1 and DC101) either alone or in combination, while those left untreated served as tumor controls. Tumor volume and animal survival time were analyzed to evaluate the outcome of different treatment modalities. In addition, the immunohistochemical expression of VEGF in the brain adjacent to the tumor, von Willebrand factor (vWF), apoptotic, and proliferative markers in the tumor area were examined. PDT or MF1 + DC101 alone significantly reduced the tumor volume and prolonged the survival time of glioma‐implanted animals. Combined therapy markedly reduced tumor volume and increased survival time with significantly better outcomes than both monotherapies. Both vWF and VEGF levels significantly increased after PDT while they both significantly decreased after antiangiogenic treatment, compared with no treatment. PDT plus antiangiogenic treatment led to significant decreases in both vWF and VEGF expression, compared with PDT alone. Either PDT or antiangiogenic treatment alone significantly increased tumor cell apoptosis compared with no treatment, while combination therapy resulted in further augmentation of apoptosis. Antiangiogenic treatment with or without PDT significantly decreased tumor cell proliferation, compared with either no treatment or PDT alone. In summary, we demonstrate both significant inhibition of tumor growth and extended survival of mice treated by the combination therapy with PDT and antiangiogenic agents, compared with each single treatment, suggesting that the combination therapy may be a promising strategy to improve clinical outcomes in glioblastoma.
Value of ANCA measurements during remission to predict a relapse of ANCA-associated vasculitis--a meta-analysis.

OBJECTIVE The value of repeated ANCA measurements among patients with an established diagnosis of ANCA-associated vasculitis (AAV) remains controversial. The aim of this study was to explore whether either of the two distinct patterns of ANCA values during remission, a rise in ANCA or persistently positive ANCA, predicted future relapse. METHODS MEDLINE and EMBASE searches were performed. Studies with at least 10 subjects with AAV from which both sensitivity and specificity of a rise in ANCA and/or persistent ANCA for future disease relapse could be calculated were included. Likelihood ratios were calculated for each study and pooled to arrive at summary estimates. I(2)-values were calculated as a measure of heterogeneity and meta-regression was used to explore sources of heterogeneity. RESULTS Nine articles on a rise in ANCA and nine articles on persistent ANCA were included. The summary estimates for positive likelihood ratio (LR(+)) and negative likelihood ratio (LR(-)) of a rise in ANCA during remission on subsequent relapse of disease were 2.84 (95% CI 1.65, 4.90) and 0.49 (95% CI 0.27, 0.87), respectively. The summary estimates for LR(+) and LR(-) of persistent ANCA during remission for subsequent disease relapse were 1.97 (95% CI 1.43, 2.70) and 0.73 (95% CI 0.50, 1.06), respectively. There was substantial between-study heterogeneity, which was partially explained by the frequency of ANCA measurements. CONCLUSION Among patients with AAV, a rise in or persistence of ANCA during remission is only modestly predictive of future disease relapse. There is limited use to serial ANCA measurements during disease remission to guide treatment decisions for individual patients with AAV.
Capturing Upper Body Motion in Conversation: An Appearance Quasi-Invariant Approach

We address the problem of body communication retrieval and measuring in seated conversations by means of markerless motion capture. In psychological studies, the use of automatic methods is key to reduce the subjectivity present in manual behavioral coding used to extract these cues. These studies usually involve hundreds of subjects with different clothing, non-acted poses, or different distances to the camera in uncalibrated, RGB-only video. However, range cameras are not yet common in psychology research, especially in existing recordings. Therefore, it becomes highly relevant to develop a fast method that is able to work in these conditions. Given the known relationship between depth and motion estimates, we propose to robustly integrate highly appearance-invariant image motion features in a machine learning approach, complemented with an effective tracking scheme. We evaluate the method's performance with existing databases and a database of upper body poses displayed in job interviews that we make public, showing that in our scenario it is comparable to that of Kinect without using a range camera, and state-of-the-art w.r. t. the HumanEva and ChaLearn 2011 evaluation datasets.
Moral Reasoning and Moral Behavior Among Selected Groups of Practicing Nurses

This study examined the relationship between moral reasoning and moral behavior in 79 practicing nurses. Moral reasoning was measured by Rest's Defining Issues Test. Judgments about Nursing Decisions (JAND), developed by the investigator, was used to measure moral behavior. JAND is comprised of seven stories, each depicting a nurse in an ethical dilemma, with a total of 48 items. It measures two components of moral behavior: knowledge and valuation of ideal moral behavior and perception of realistic moral behavior. The hypothesis that moral reasoning would be positively related to knowledge and valuation of ideal moral behavior was tested by Pearson product moment correlation; the obtained coefficient of . 28 was significant at the . 01 level. The hypothesis that moral reasoning would be positively related to nurses' perception of realistic moral behavior was also tested by Pearson product moment correlation; the obtained coefficient of . 19 was significant at the . 05 level. Additional analyses showed significant differences in the knowledge and valuation component of JAND between educational groups, ethnic groups, age groups, and years of practice in nursing; but, there were no differences between these groups with respect to the perception of realistic moral behavior component of JAND. Implications of the findings for nursing practice, education, and research are discussed.
Neural stimulation with optical radiation

This paper reviews the existing research on infrared neural stimulation, a means of artificially stimulating neurons that has been proposed as an alternative to electrical stimulation. Infrared neural stimulation (INS) is defined as the direct induction of an evoked potential in response to a transient targeted deposition of optical energy. The foremost advantage of using optical radiation for neural stimulation is its spatial resolution. Exogenously applied or trans‐genetically synthesized fluorophores are not used to achieve stimulation. Here, current work on INS is presented for motor nerves, sensory nerves, central nervous system, and in vitro preparations. A discussion follows addressing the mechanism of INS and its potential use in neuroprostheses. A brief review of neural depolarization involving other optical methods is also presented. Topics covered include optical stimulation concurrent with electrical stimulation, optical stimulation using exogenous fluorophores, and optical stimulation by transgenic induction of light‐gated ion channels.
article : autoimmune hepatitis – current management and challenges

Results Autoimmune hepatitis has a global distribution affecting any age, both sexes and all ethnic groups. Clinical manifestations are variable ranging fromno symptoms to severe acute hepatitis and only seldom to fulminant hepatic failure. Autoimmune attack is perpetuated, possibly via molecular mimicry mechanisms, and favoured by the impaired control of regulatory T-cells. A typical laboratory finding is hypergammaglobulinaemia with selective elevation of IgG, although in 15– 25% of patients – particularly children, elderly and acute cases – IgG levels are normal. Liver histology and autoantibodies, although not pathognomonic, still remain the hallmark for diagnosis. Immunosuppressive treatment is mandatory and life-saving; however, to meet strict response criteria, the conventional therapy with prednisolone with or without azathioprine is far from ideal.
A Multicenter Evaluation of the Performance and Usability of a Novel Glucose Monitoring System in Chinese Adults With Diabetes

Objective: Flash glucose monitoring is a new glucose sensing technique that measures interstitial glucose levels for up to 14 days and does not require any calibration. The aim of this study is to evaluate the performance of the new system in Chinese patients with diabetes. Methods: A multicenter, prospective, masked study was performed in a total of 45 subjects with diabetes. Subjects wore 2 sensors at the same time, for up to 14 days. The accuracy was evaluated against capillary blood glucose (BG) and venous Yellow Springs Instrument (YSI; Yellow Springs, OH) measurements. During all 14 days, subjects were asked to perform at least 8 capillary BG tests per day. Each subject attended 3 days of 8-hour clinic sessions to measure YSI and sensor readings every 15 minutes. Results: Forty subjects had evaluable glucose readings, with 6687 of 6696 (99.9%) sensor and capillary BG pairs within consensus error grid zones A and B, including 5824 (87.0%) in zone A. The 6969 sensor and venous YSI pairs resulted in 6965 (99.9%) pairs within zones A and B, including 5755 (82.6%) in zone A. The sensor pairs with BG and YSI result in mean absolute relative difference (MARD) of 10.0% and 10.7%, respectively. Overall between-sensor coefficient of variation (CV) was 8.0%, and the mean lag time was 3.1 (95% confidence interval 2.54 to 4.29) minutes. Conclusions: The system works well for people with diabetes in China, and it is easy to wear and use.
Transition Metal Impurities in Semiconductors: Induced Magnetism and Band Gap Engineering

The main subject of this thesis is the study of electronic and magnetic properties of materials containing 3d transition metal atoms. Our motivation stems mainly from the modern fields of spintronic computing and solar energy conversion. The two primary goals of this work are to determine (i) why certain transition metal impurities in certain semiconductors can induce magnetic properties suitable for spintronic computing applications, and (ii) how transition metal impurities can be used to modify the electronic band gaps of semiconductors and insulators in ways useful for harnessing solar energy and for other applications. To accomplish these goals, we have applied both experimental and theoretical tools. We studied high quality materials prepared by advanced synthesis techniques using x-ray spectroscopy methods at synchrotron light sources. The results of these experiments were interpreted using a variety of theoretical techniques, primarily using computational software developed as part of this thesis and discussed herein. Regarding the study of introducing transition metal impurities into semiconductors to induce magnetic properties, we first developed and demonstrated a method to determine the location of impurity atoms within the host semiconductor lattice. This allowed to us explain the presence and absence of ferromagnetism in samples prepared under only slightly different synthesis conditions, which helped to address some long–standing issues in the spintronics field. We then studied an advanced and promising material—indium (III) oxide with iron impurities—to determine how magnetic ordering was maintained up to room temperatures. Our techniques unveiled that a portion of the iron atoms were coupled to oxygen vacancies in the material to create conditions which propelled the observed magnetism. This finding confirmed some earlier theoretical predictions by others in the field. For the study of electronic band gap modifications in semiconductors and insulators via the incorporation of transition metal atoms, we investigated a wide range of materials synthesized using different techniques. Again, we used experimental techniques to determine the location of impurity atoms within the materials, and used this to understand how band gaps were modified upon the introduction of the impurities. For Ti implantation into SiO2, Ni substitution into ZnO, and a new material, MnNCN, we have determined the electronic band gaps and used our techniques to explain how the values for the gaps arise. Finally, an additional outcome of this thesis work is a software program capable of simulating x-