Miracle-dz/UniFAR-FTUs huggingface dataset:
Candida albicans cell walls contain the fluorescent cross-linking amino acid dityrosine

Several clinical and laboratory isolates of Candida albicans have a natural blue surface fluorescence when cultured and observed with sensitive optics. The localization and color of the fluorescence are similar to those of the natural fluorescence of sporulated Saccharomyces cerevisiae which is caused by the generation and surface deposition of the cross-linking amino acid dityrosine. In S. cerevisiae, dityrosine production results from the direct action of at least two genes and is responsible for resistance of the ascospores to lytic enzymes and physicochemical trauma. Among the criteria for the identification of dityrosine is pH sensitivity of the fluorescence intensity and a highly characteristic shift of the fluorescence excitation maximum with a change in pH. Video microscopy of whole Candida organisms revealed the characteristic dityrosine intensity maximum at pH approximately 10 and the intensity minimum at pH approximately 2. Separation of an acid hydrolysate of Candida cell walls by reverse-phase high-performance liquid chromatography revealed a fluorescence peak that coelutes with the reagent dityrosine. At pH approximately 10, this peak has a fluorescence excitation maximum of 320 to 325 nm, while at pH approximately 2, the excitation maximum is 285 to 290 nm. This excitation maximum shift and the observed emission maximum of approximately 410 nm are characteristic of dityrosine. Two separate strains of C. albicans were injected intraperitoneally into mice and harvested at 24 h. Blue surface fluorescence was observed, suggesting that dityrosine generation occurs in vivo as well as in vitro. This is the first report of the presence of dityrosine in a human fungal pathogen.
Modeling of the dispensing-based tissue scaffold fabrication processes

Tissue engineering is an emerging area with an aim to create artificial tissues or organs by employing methods of biology, engineering and material science. In tissue engineering, scaffolds are three-dimensional (3D) structure made from biomaterials with highly interconnected pore networks or microstructure, and are used to provide the mechanical and biological cues to guide cell differentiation in order to form desired three-dimensional tissues or functional organs. Hence, tissue scaffold plays a critical role in tissue engineering. However, fabrication of such scaffolds has proven to be a challenge task. One important barrier is the inability to fabricate scaffolds with designed pore size and porosity to mimic the microstructure of native tissue. Another issue is the prediction of process-induced cell damage in the cell-involved scaffold fabrication processes. By addressing these key issues involved in the scaffold fabrication, this research work is aimed at developing methods and models to represent the dispensing-based solid free form scaffold fabrication process with and without the presence of living cells. The microstructure of scaffolds, featured by the pore size and porosity, has shown to significantly affect the biological and mechanical properties of formed tissues. As such, during fabrication process the ability to predict and determine scaffold pore size and porosity is of great importance. In the first part of this research, the flow behaviours of the scaffold materials were investigated and a model of the flow rate of material dispensed during the scaffold fabrication was developed. On this basis, the pore size and porosity of the scaffolds fabricated were represented by developing a mathematical model. Scaffold fabrication experiments using colloidal gels with different hydroxylapatite volume fractions were carried out and the results obtained agreed with those from model simulations, indicating the effectiveness of the models
Triaxial failure criterion for concrete and its generalization

The authors present a failure criterion that describes the triaxial strength of concrete in terms of three independent stress invariants. Its geometric representation in principal stress space is convex and smooth and is characterized by two parabolic meridians and a deviatoric section that changes from triangular to circular shape with increasing confinement. The three-parameter description is calibrated from elementary strength data of uniaxial compression and uniaxial tension, as well as equibiaxial compression experiments. The failure criterion is verified with different biaxial and triaxial strength data on plain concrete. Finally, the failure criterion is generalized to a format that includes the standard strength hypotheses of Huber-Mises, Drucker-Prager, Rankine, Mohr-Coulomb, and Leon as special cases.
Making sense of UML class model changes by textual difference presentation

Understanding the difference between two models, such as different versions of a design, can be difficult. It is a commonly held belief that the best way of presenting a model difference is by using graph or tree-based visualizations. We disagree and present an alternative approach where sets of low-level model differences are abstracted into high-level model differences that lend themselves to being presented textually. The results of preliminary user studies support our claim.
VELA X-1 AS SEEN BY RXTE

We present results from four observations of the ac- creting X-ray pulsar Vela X-1 with the Rossi X-ray Timing Explorer (RXTE) in 1996 February. The light curves show strong pulse to pulse variations, while the average pulse profiles are quite stable, similar to previous results. Below 5 keV the pulse profiles display a complex, 5- peaked structure with a transition to a simple, double peak above 15 keV. We analyze phase-averaged, phase-resolved, and on-pulse minus off-pulse spectra. The best spectral fits were obtained using continuum models with a smooth high-energy turnover. In contrast, the commonly used power law with exponential cutoff introduced artificial features in the fit residuals. Using a power law with a Fermi-Dirac cutoff modified by photoelectric absorption and an iron line, the best fit spectra are still unaccept- able. We interpret large deviations around 25 and55 keV as fundamental and second harmonic cyclotron absorption lines. If this result holds true, the ratio of the line energies seems to be larger than 2. Phase resolved spectra show that the cyclotron lines are strongest on the main pulse while they are barely visible outside the pulses.
Investigation of interface traps located at different regions in p-MOS transistors using DCIV technique

The interface traps located at different regions along the Si/SiO/sub 2/ interface, i.e., base channel (BC), drain junction-space-charge (JSC) and gate-drain extension (DE) overlap regions in p-MOS transistors are investigated by the newly developed direct-current current-voltage (DCIV) technique. When the gate voltage is swept from a low negative to a high positive value, two thermal recombination current peaks and one thermal-trap-tunneling (TTT) peak are formed, corresponding to the interface traps located at BC, JSC and DE regions, respectively. Interactions of interface traps located at different regions are observed when applying different kinds of stresses. The generation of interface traps in one region may cause reduction and migration of interface traps in another. This effect is interpreted by a hydrogen release and absorption model and may have profound influence upon device lifetime projection.
Randomized Controlled Trial of Prophylactic Phenytoin after Neurosurgery for Brain Tumor

Add-on Phenytoin Fails to Prevent Early Seizures after Surgery for Supratentorial Brain Tumors: A Randomized Controlled Study De Santis A, Villani R, Sinisi M, Stocchetti N, Perucca E Epilepsia 2002;43:175–182 Purpose To determine the potential effectiveness of phenytoin (PHT) in preventing early postoperative seizures in patients undergoing craniotomy for supratentorial brain tumors. Two hundred patients requiring elective craniotomy for supratentorial brain tumors were randomized to two groups of equal size, with a prospective, open-label, controlled design. One group received PHT (18 mg/kg as an intravenous intraoperative load, followed by additional daily doses aimed at maintaining serum PHT concentrations within the 10- to 20-age/ml range) for 7 consecutive days. In the other group, PHT was not administered. More than 90% of patients in both groups continued to take preexisting anticonvulsant medication (AEDs) with carbamazepine or phenobarbital throughout the study. The primary efficacy end point was the number of patients remaining free from seizures during the 7-day period after the operation. Of 100 patients allocated to PHT, 13 experienced seizures during the 7-day observation period, compared with 11 of 100 patients in the placebo group (p > 0.05). Most seizures occurred in the first day after surgery in both groups. There were no differences between groups in the proportion of patients experiencing more than one seizure, but there was a trend for generalized seizures to be more common in PHT-treated patients than in controls (11 vs. five patients, respectively). Status epilepticus occurred in one patient in the PHT group and in two patients in the control group. Of the 13 PHT-treated seizure patients, 11 had serum PHT concentrations within the target range, and only two had concentrations below range on the days their seizures occurred. PHT, given at dosages producing serum concentrations within the target range, failed to prevent early postoperative seizures in patients treated with concomitant AEDs. Prophylactic administration of PHT cannot be recommended in these patients.
The RING-Finger Ubiquitin Ligase HAF1 Mediates Heading date 1 Degradation during Photoperiodic Flowering in Rice[OPEN]

HAF1 plays a pivotal role in promotion of flowering through regulation of Hd1 accumulation during photoperiod response in rice. The photoperiodic response is one of the most important factors determining heading date in rice (Oryza sativa). Although rhythmic expression patterns of flowering time genes have been reported to fine-tune the photoperiodic response, posttranslational regulation of key flowering regulators has seldom been elucidated in rice. Heading date 1 (Hd1) encodes a zinc finger transcription factor that plays a crucial role in the photoperiodic response, which determines rice regional adaptability. However, little is known about the molecular mechanisms of Hd1 accumulation during the photoperiod response. Here, we identify a C3HC4 RING domain-containing E3 ubiquitin ligase, Heading date Associated Factor 1 (HAF1), which physically interacts with Hd1. HAF1 mediates ubiquitination and targets Hd1 for degradation via the 26S proteasome-dependent pathway. The haf1 mutant exhibits a later flowering heading date under both short-day and long-day conditions. In addition, the haf1 hd1 double mutant headed as late as hd1 plants under short-day conditions but exhibited a heading date similar to haf1 under long-day conditions, thus indicating that HAF1 may determine heading date mainly through Hd1 under short-day conditions. Moreover, high levels of Hd1 accumulate in haf1. Our results suggest that HAF1 is essential to precise modulation of the timing of Hd1 accumulation during the photoperiod response in rice.
A Visual Interface for Building SPARQL Queries in Konduit

This short demo description presents an extension to the Konduit tool for visual programming for the semantic desktop. Previously, Konduit required users to define filter components by manually specifying a SPARQL CONSTRUCT query. With the current work presented in this demo, we are exploring ways of building such queries visually, and aiding the use in doing it. We hope that this will make it easier to work with Konduit, which will thus appeal to more users.
CUDA Accelerated LTL Model Checking

Recent technological developments made available various many-core hardware platforms. For example, a SIMD-like hardware architecture became easily accessible for many users who have their computers equipped with modern NVIDIA GPU cards with CUDA technology. In this paper we redesign the maximal accepting predecessors algorithm [7] for LTL model checking in terms of matrix-vector product in order to accelerate LTL model checking on many-core GPU platforms. Our experiments demonstrate that using the NVIDIA CUDA technology results in a significant speedup of verification process.
Building a better bacillus: the emergence of Mycobacterium tuberculosis

The genus Mycobacterium is comprised of more than 150 species that reside in a wide variety of habitats. Most mycobacteria are environmental organisms that are either not associated with disease or are opportunistic pathogens that cause non-transmissible disease in immunocompromised individuals. In contrast, a small number of species, such as the tubercle bacillus, Mycobacterium tuberculosis, are host-adapted pathogens for which there is no known environmental reservoir. In recent years, gene disruption studies using the host-adapted pathogen have uncovered a number of “virulence factors,” yet genomic data indicate that many of these elements are present in non-pathogenic mycobacteria. This suggests that much of the genetic make-up that enables virulence in the host-adapted pathogen is already present in environmental members of the genus. In addition to these generic factors, we hypothesize that molecules elaborated exclusively by professional pathogens may be particularly implicated in the ability of M. tuberculosis to infect, persist, and cause transmissible pathology in its host species, Homo sapiens. One approach to identify these molecules is to employ comparative analysis of mycobacterial genomes, to define evolutionary events such as horizontal gene transfer (HGT) that contributed M. tuberculosis-specific genetic elements. Independent studies have now revealed the presence of HGT genes in the M. tuberculosis genome and their role in the pathogenesis of disease is the subject of ongoing investigations. Here we review these studies, focusing on the hypothesized role played by HGT loci in the emergence of M. tuberculosis from a related environmental species into a highly specialized human-adapted pathogen.
Study on mechanical, micro-, and macrostructural characteristics of dissimilar friction stir welding of AA6061-T6 and AA7075-T6

Abstract This research presents the effect of welding speed on dissimilar joints of AA7075-T6 and AA6061-T6 alloys. The weld quality was evaluated through observations of the macrostructure. The mechanical properties of the welds, including the ultimate strength, the percentage of elongation, and the microhardness variations, were determined for different welding speeds. Also the effect of the positions of the two alloys on the mechanical properties was investigated. In addition, during the friction stir welding (FSW) process, the peak temperatures were measured in order to indicate the relation between the peak temperature and the hardness distribution at the heat-affected zone (HAZ). Accordingly, the influence of the welding speed on the developed grain size was elucidated by the microstructural analysis.
Misreporting of energy and micronutrient intake estimated by food records and 24 hour recalls, control and adjustment methods in practice

In order to assess nutritional adequacy, valid estimates of nutrient intake are required. One of the main errors in dietary assessment is misreporting. The objective was to review the extent, nature and determinants of misreporting in dietary assessment, how this affects reported intakes of micronutrients and how this is identified and measured, and to identify the best ways of dealing with misreporting when interpreting results. A systematic literature search was conducted for studies of misreporting of dietary intake in adults by 24 hour recalls or by estimated or weighed food records, published up to March 2008. Thirty-seven relevant studies were identified. Possible causes of misreporting were identified. Methods most used to identify misreporting were the Goldberg cut-off (46 % studies) and the doubly labelled water technique (24 % studies). The magnitude of misreporting of energy intake was similar in all three dietary assessment methods. The percentage of under-reporters was about 30 % and energy intake was underestimated by approximately 15 %. Seven papers presented usable data for micronutrient intake. Absolute intakes of Fe, Ca and vitamin C (the three micronutrients addressed in all papers) were on average 30 % lower in low-energy reporters (LER) than that in non-LER and, although results were not consistent, there was a tendency for micronutrient density to be higher in LER. Excluding underreporters or using energy adjustment methods for micronutrient intakes is discussed. Residual method of energy adjustment seems to be a good tool for practice to decrease an influence of misreporting when interpreting results of studies based on food records and 24 hour recalls.
Design and optimizations of asymmetric solenoid type magnetic coupler in wireless charging system for electric vehicles

This paper focuses on the design of the magnetic coupler in the wireless charging system for electric vehicles. A solenoid type magnetic coupler is used for the better ability of magnetic coupling than the plate type magnetic coupler under the condition of mid-range wireless power transfer. The factors of coupling coefficient are analyzed in two kinds of ways, magnetic circuit theory and mutual inductance theory. A solenoid type magnetic coupler with new core structure design and new winding design is proposed in consideration of coupling coefficient, utilization factor of core, winding distribution, horizontal position misalignment and horizontal angle misalignment. The whole design meets the requirements of 3.3 kW wireless charging system and is simulated by 3D finite element analysis software.
Ets‐1 immunohistochemical expression in non‐melanoma skin carcinoma

Background: Ets‐1 oncoprotein is a transcription factor known to regulate the expression of numerous genes important in extracellular matrix remodeling and angiogenesis. Up‐regulation of Ets‐1 has been shown to be important in a variety of human malignancies and to correlate with prognosis. To our knowledge, this oncoprotein has not been examined in non‐melanoma skin carcinomas.
Current Treatment Strategies for Intracranial Aneurysms: An Overview

Intracranial aneurysm is a leading cause of stroke. Its treatment has evolved over the past 2 decades. This review summarizes the treatment strategies for intracranial aneurysms from 3 different perspectives: open surgery approach, transluminal treatment approach, and new technologies being used or trialed. We introduce most of the available treatment techniques in detail, including contralateral clipping, wrapping and clipping, double catheters assisting coiling and waffle-cone technique, and so on. Data from major trials such as Analysis of Treatment by Endovascular approach of Non-ruptured Aneurysms (ATENA), Internal Subarachnoid Trial (ISAT), Clinical and Anatomical Results in the Treatment of Ruptured Intracranial Aneurysms (CLARITY), and Barrow Ruptured Aneurysm Trial (BRAT) as well as information from other clinical reports and local experience are reviewed to suggest a clinical pathway for treating different types of intracranial aneurysms. It will be a valuable supplement to the current existing guidelines. We hope it could help assisting real-time decision-making in clinical practices and also encourage advancements in managing the disease.
Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin

The dynamic composition of proteins associated with nuclear DNA is a fundamental property of chromosome biology. In the chromatin compartment dedicated protein complexes govern the accurate synthesis and repair of the genomic information and define the state of DNA compaction in vital cellular processes such as chromosome segregation or transcription. Unscheduled or faulty association of protein complexes with DNA has detrimental consequences on genome integrity. Consequently, the association of protein complexes with DNA is remarkably dynamic and can respond rapidly to cellular signaling events, which requires tight spatiotemporal control. In this context, the ring-like AAA+ ATPase CDC48/p97 emerges as a key regulator of protein complexes that are marked with ubiquitin or SUMO. Mechanistically, CDC48/p97 functions as a segregase facilitating the extraction of substrate proteins from the chromatin. As such, CDC48/p97 drives molecular reactions either by directed disassembly or rearrangement of chromatin-bound protein complexes. The importance of this mechanism is reflected by human pathologies linked to p97 mutations, including neurodegenerative disorders, oncogenesis, and premature aging. This review focuses on the recent insights into molecular mechanisms that determine CDC48/p97 function in the chromatin environment, which is particularly relevant for cancer and aging research.
Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin

Significance It has been accepted dogma that eukaryotes and heme-synthesizing bacteria use the same metabolic intermediates in their heme synthesis pathways, where protoporphyrin is the final intermediate into which iron is inserted to make protoheme. Herein, we present data demonstrating that Gram-positive bacteria do not use protoporphyrin as an intermediate but, instead, have an altered set of terminal reactions that oxidize coproporphyrinogen to coproporphyrin and insert ferrous iron into coproporphyrin, resulting in the formation of coproheme. A newly characterized enzyme, HemQ, decarboxylates coproheme to generate protoheme. Because some organisms that possess this coproporphyrin-dependent branch are major causes of human disease, HemQ is a novel pharmacological target of significant therapeutic relevance, particularly given high rates of antimicrobial resistance among these pathogens. It has been generally accepted that biosynthesis of protoheme (heme) uses a common set of core metabolic intermediates that includes protoporphyrin. Herein, we show that the Actinobacteria and Firmicutes (high-GC and low-GC Gram-positive bacteria) are unable to synthesize protoporphyrin. Instead, they oxidize coproporphyrinogen to coproporphyrin, insert ferrous iron to make Fe-coproporphyrin (coproheme), and then decarboxylate coproheme to generate protoheme. This pathway is specified by three genes named hemY, hemH, and hemQ. The analysis of 982 representative prokaryotic genomes is consistent with this pathway being the most ancient heme synthesis pathway in the Eubacteria. Our results identifying a previously unknown branch of tetrapyrrole synthesis support a significant shift from current models for the evolution of bacterial heme and chlorophyll synthesis. Because some organisms that possess this coproporphyrin-dependent branch are major causes of human disease, HemQ is a novel pharmacological target of significant therapeutic relevance, particularly given high rates of antimicrobial resistance among these pathogens.
Slippage of Mitotic Arrest and Enhanced Tumor Development in Mice with BubR1 Haploinsufficiency

A compromised spindle checkpoint is thought to play a key role in genetic instability that predisposes cells to malignant transformation. Loss of function mutations of BubR1, an important component of the spindle checkpoint, have been detected in human cancers. Here we show that BubR1+/− mouse embryonic fibroblasts are defective in spindle checkpoint activation, contain a significantly reduced amount of securin and Cdc20, and exhibit a greater level of micronuclei than do wild-type cells. RNA interference-mediated down-regulation of BubR1 also greatly reduced securin level. Moreover, compared with wild-type littermates, BubR1+/− mice rapidly develop lung as well as intestinal adenocarcinomas in response to challenge with carcinogen. BubR1 is thus essential for spindle checkpoint activation and tumor suppression.