Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico prediction and immunological validation of common HLA‐DRB1‐restricted T cell epitopes of Candida albicans secretory aspartyl proteinase 2

Sap2 is the most abundant virulence factor expressed during Candida infection, and the principal protein known to induce antibody response during Candida infection in humans. Its role in T‐cell activation however, has not yet been determined. Sequence analysis revealed that Sap2 contains two variable regions: Var1 and Var2. Computational predictions by the Hotspot Hunter program identified that Var1 contains three candidate T‐cell epitopes, whereas Var2 contains four. Thirty‐nine overlapping peptides of Sap2 were then synthesized, and tested for their ability to induce proliferation of PBMC from 12 donors. Peptides P11, P17 and P31 exhibited significantly higher proliferative indices when compared with those of other peptides or controls. P17 and P31 are located in the areas of prediction, while P11 is not. There were other peptides outside the prediction areas that could stimulate PBMC proliferation at low levels. Nevertheless, the proliferative noise caused by such peptides was ruled out by IL‐2 ELISpot analysis. Only P17 and P31 were shown to induce clonal proliferation of IFN‐γ producing lymphocytes, suggesting that these two peptides contain T cell epitopes. P11, which stimulated IL‐2 producing clones, contains a known B‐cell epitope. Interestingly, P17 and P31 elicited both Th1 and Th2 cell responses with significant numbers of IL‐13 secreting clones in response to stimulation. Taken together, the computer‐based T cell epitope prediction method could identify the immunogenic T cell epitopes of C. albicans Sap2 that promiscuously bind to the HLA‐DRB1 supertype.
A Tensor-based Factorization Model of Semantic Compositionality

In this paper, we present a novel method for the computation of compositionality within a distributional framework. The key idea is that compositionality is modeled as a multi-way interaction between latent factors, which are automatically constructed from corpus data. We use our method to model the composition of subject verb object triples. The method consists of two steps. First, we compute a latent factor model for nouns from standard co-occurrence data. Next, the latent factors are used to induce a latent model of three-way subject verb object interactions. Our model has been evaluated on a similarity task for transitive phrases, in which it exceeds the state of the art.
NOVEL CO-PROCESSED SUPERDISINTEGRANTS IN THE DESIGN OF FAST DISSOLVING TABLETS

In the present study, novel co-processed superdisi ntegrants were developed by solvent evaporation method using crospovidone and sodium starch glycolate in different ratios (1:1, 1:2 & 1:3) for use in the fast dissolving tablet formulations. The developed excip ients were evaluated for angle of repose, Carr’s in dex and Hausner’s ratio in comparison with physical mixture of superdisintegrants. The angle of repose of the developed excipients was found to be < 25 o , Carr’s index in the range of 10-15% and Hausner’s ratio in the range of 1.13-1.16. Fast dissolving tablets of meto clopramide hydrochloride were prepared using the above coprocessed superdisintegrants and evaluated for pre- compression and post-compression parameters. Based on in vitro dispersion time (approximately 19 sec), promising formulation CP 1 was tested for in vitro drug release pattern in pH 6.8 Phosphate buffer, short-term stab ility (at 40 0 C/75% RH for 3 months) and drug excipient interaction (IR spectroscopy). Among the designed f ormulations, the formulation (CP 1) containing 4% w/w of co-processed superdisintegrant (1:1 mixture of cro spovidone and sodium starch glycolate) emerged as t he overall best formulation (t 50% 1.30 min) based on drug release characteristics in pH 6.8 phosphate buffer compared to commercial conventional tablet formulation (t 50% 6 min). Short-term stability studies on promising formulation indicated that there were no significan t changes in drug content and in vitro dispersion time (p<0.05).
Inhibition of Heme Oxygenase-1 Increases Responsiveness of Pancreatic Cancer Cells to Anticancer Treatment

Heme oxygenase-1 (HO-1) is believed to represent a key enzyme for the protection of cells against “stress. ” Its overexpression in different types of human cancers supports the notion that HO-1 provides a growth advantage and contributes to cellular resistance against chemotherapy and radiotherapy. Given the poor survival rates of patients with pancreatic cancer due to its aggressive growth behavior and its exceptional resistance to all known forms of anticancer treatment, we have investigated the expression of HO-1 in human pancreatic cancer cells growth behavior and prognosis. Expression of HO-1 was analyzed in human pancreatic cancer samples in comparison with normal pancreas by quantitative PCR, Western blot, and confocal microscopy. The influence of radiotherapy and chemotherapy on HO-1 expression in pancreatic cancer cell lines was evaluated. Furthermore, HO-1 expression was specifically suppressed by small interfering RNA transfection and subsequently the alterations of growth behavior and resistance to anticancer treatment were tested. Human pancreatic cancer showed a 6-fold and 3.5-fold HO-1 up-regulation in comparison to normal pancreas based on mRNA and protein level, respectively (P < 0.05). Cancer tissues revealed marked HO-1 immunoreactivity in tumor cells and in tumor associated immunocytes. Treatment of the pancreatic cancer cell lines with gemcitabine or radiation strongly induced HO-1 expression. Targeted knockdown of HO-1 expression led to pronounced growth inhibition of the pancreatic cancer cells and made tumor cells significantly more sensitive to radiotherapy and chemotherapy. Therefore, specific inhibition of HO-1 expression may be a new option in pancreatic cancer therapy and may be used as sensitizer to chemotherapy and radiotherapy.
Thoracoabdominal Computed Tomography in Trauma Patients: A Cost-Consequences Analysis

Background: CT is increasingly used during the initial evaluation of blunt trauma patients. In this era of increasing cost-awareness, the pros and cons of CT have to be assessed. Objectives: This study was performed to evaluate cost-consequences of different diagnostic algorithms that use thoracoabdominal CT in primary evaluation of adult patients with high-energy blunt trauma. Materials and Methods: We compared three different algorithms in which CT was applied as an immediate diagnostic tool (rush CT), a diagnostic tool after limited conventional work-up (routine CT), and a selective tool (selective CT). Probabilities of detecting and missing clinically relevant injuries were retrospectively derived. We collected data on radiation exposure and performed a micro-cost analysis on a reference case-based approach. Results: Both rush and routine CT detected all thoracoabdominal injuries in 99.1% of the patients during primary evaluation (n = 1040). Selective CT missed one or more diagnoses in 11% of the patients in which a change of treatment was necessary in 4.8%. Rush CT algorithm costed € 2676 (US$ 3660) per patient with a mean radiation dose of 26.40 mSv per patient. Routine CT costed € 2815 (US$ 3850) and resulted in the same radiation exposure. Selective CT resulted in less radiation dose (23.23 mSv) and costed € 2771 (US$ 3790). Conclusions: Rush CT seems to result in the least costs and is comparable in terms of radiation dose exposure and diagnostic certainty with routine CT after a limited conventional work-up. However, selective CT results in less radiation dose exposure but a slightly higher cost and less certainty.
The Role of Bioacoustic Signals in Koala Sexual Selection: Insights from Seasonal Patterns of Associations Revealed with GPS-Proximity Units

Despite being a charismatic and well-known species, the social system of the koala (Phascolarctos cinereus—the only extant member of the family Phascolarctidae) is poorly known and much of the koala’s sociality and mating behaviors remain un-quantified. We evaluated these using proximity logging-GPS enabled tracking collars on wild koalas and discuss their implications for the mating system of this species. The frequency and duration of male-female encounters increased during the breeding season, with male-male encounters quite uncommon, suggesting little direct mating competition. By comparison, female-female interactions were very common across both seasons. Body mass of males was not correlated with their interactions with females during the breeding season, although male size is associated with a variety of acoustic parameters indicating individuality. We hypothesise that vocal advertising reduces the likelihood of male-male encounters in the breeding season while increasing the rate of male-female encounters. We suggest that male mating-season bellows function to reduce physical confrontations with other males allowing them to space themselves apart, while, at the same time, attracting females. We conclude that indirect male-male competition, female mate choice, and possibly female competition, mediate sexual selection in koalas.
Use of Fascia Component of the Anterolateral Thigh Flap for Different Reconstructive Purposes

The anterolateral thigh flap is commonly used for reconstruction of soft-tissue defects located at various sites of the body. This versatile flap offers many advantages to the reconstructive microsurgeons for the treatment of difficult defects. From 2000 to 2005, 70 anterolateral thigh flaps were transferred to reconstruct soft-tissue defects. We retrospectively reviewed these patients and found that the fascia lata component of the flap was used for different purposes in 19 patients. The fascia lata component of the flap was used for suspension of the flap in lip reconstruction in 12 patients, for reconstruction of dural defect in the scalp in 2 patients, for reconstruction of tendon defects in the forearm in 3 patients, and for reconstruction of fascia defect in the abdominal wall in the remaining 2. Complete loss of the flap was seen in an anterolateral thigh flap (5.2%) that was used for lower lip reconstruction. One flap necrosed partially (5.2%), and it was treated with surgical debridement and transposition of latissimus dorsi musculocutaneous flap. The objective of this study is to focus on the reliability of the fascial component of the anterolateral thigh flap. Although many authors have described other advantages of the anterolateral thigh flap extensively, this peculiarity has not been stressed adequately. Anterolateral thigh flap offers a thick and vascular fascial component with large amounts that can be used for different reconstructive purposes, and it should be taken into consideration as an important advantage of the flap, together with other well-known advantages.
Effects of time and watershed characteristics on the concentration of Cryptosporidium oocysts in river water

Water samples were collected from four locations on two rivers in Washington State and analyzed by membrane filtration-immunofluorescence assay to establish Cryptosporidium oocyst concentrations. Sampling locations were selected to evaluate effects of watershed character, from pristine mountain to downstream agricultural, on oocyst concentrations. Samples were collected at six biweekly intervals from late June to early September, with two additional sets of five samples taken on separate days (one set taken at bihourly intervals and one set taken simultaneously). Cryptosporidium oocysts were found in 34 of 35 samples at concentrations ranging from about 0.2 to 65 oocysts per liter. Oocyst concentrations were highest early in the sampling period, when they were influenced by postrainfall runoff, and decreased through the summer months. Oocyst concentrations found in ten samples collected on two days (5 samples per day) showed no short-term variations. Oocyst concentrations and oocyst production per square mile (ca. 2.6 km2) of watershed found in water draining a controlled public water supply watershed were the lowest observed. The concentrations and production rates for drainage from an adjacent, comparable, but uncontrolled watershed were nearly 10 times higher. The concentration and production rates of the downstream area influenced by dairy farming were nearly 10 times higher than rates at the upstream stations. The data showed clearly that oocyst concentrations were consistently observed above the detection limit of the analytical method, about 0.1 oocysts per liter; that oocyst concentrations were continuous as opposed to intermittent; and that watershed character and management affected surface water oocyst concentrations significantly.
Making Sense of Misfortune: Deservingness, Self-Esteem, and Patterns of Self-Defeat

Drawing on theorizing and research suggesting that people are motivated to view their world as an orderly and predictable place in which people get what they deserve, the authors proposed that (a) random and uncontrollable bad outcomes will lower self-esteem and (b) this, in turn, will lead to the adoption of self-defeating beliefs and behaviors. Four experiments demonstrated that participants who experienced or recalled bad (vs. good) breaks devalued their self-esteem (Studies 1a and 1b), and that decrements in self-esteem (whether arrived at through misfortune or failure experience) increase beliefs about deserving bad outcomes (Studies 1a, 1b, 2a, 2b). Five studies (Studies 3–7) extended these findings by showing that this, in turn, can engender a wide array of self-defeating beliefs and behaviors, including claimed self-handicapping ahead of an ability test (Study 3), the preference for others to view the self less favorably (Studies 4–5), chronic self-handicapping and thoughts of physical self-harm (Study 6), and choosing to receive negative feedback during an ability test (Study 7). The current findings highlight the important role that concerns about deservingness play in the link between lower self-esteem and patterns of self-defeating beliefs and behaviors. The theoretical and practical implications of these findings are discussed.
Immunocompetence of the severely injured spleen verified by differential interference contrast microscopy: the red blood cell pit test.

OBJECTIVE To determine the immunocompetence of the successfully nonoperatively managed injured spleen warranting vaccinations for overwhelming postsplenectomy sepsis by differential interference contrast microscopy (DICM). METHODS Cull an urban Level I trauma systems data bank for all patients with grade IV or V splenic injuries (those with the greatest potential to compromise immunologic function) successfully managed nonoperatively and those who have required splenectomies since 1996 and verify the Association for the Surgery of Trauma grading. Contact or obtain written consent of these patients and acquire a blood sample for DICM (red blood cell [RBC] pit analysis) and IgM levels (as a control). Compare values of those sustaining splenic injuries with those of two control groups: patients with splenectomies and those with normal splenic function. RESULTS Forty patients were contacted, consented, and volunteered blood samples: 10 patients with grade IV splenic injuries, 1 patient with a grade V injury, 14 patients with splenectomies, and 15 controls. Average RBC pit levels and IgM levels for patients sustaining injuries (15) and successfully nonoperatively managed were 0.6% (0%-2% nL) and 91 mg/dL (46-304 nL), respectively. Patients with splenectomies had levels of 20.4% and 86 mg/dL whereas controls had levels of 0.7% and 110 mg/dL, respectively. The average time frame from injury to RBC pit test was 3.1 years. Comparing the successfully nonoperatively managed group with the splenectomy group using t test with Satterthwaite's method because of unequal variances, there was a statistically significant difference (p = 0.0002). Comparing the same study group with those with normal splenic function using t test with pooled variance, there was no statistical significant difference between groups (p = 0.489). CONCLUSION DICM, a commonly used test to evaluate splenic-based immunocompetence in patients with sickle cell anemia, hemoglobinopathies, and patients undergoing partial splenectomies, also confirms splenic immunocompetence in patients sustaining up to grade IV splenic injuries. IgM levels earlier thought to be low in patients after splenectomy normalize.
Investigation of the Microbial Ecology of Intertidal Hot Springs by Using Diversity Analysis of 16S rRNA and Chitinase Genes

ABSTRACT The microbial diversity of intertidal hot springs on the seashore of northwest Iceland was examined by combining directed in situ enrichments, artificial support colonization, and mat sampling. Analysis of 16S rRNA genes revealed the presence of clones related to both marine and terrestrial, thermophilic, mesophilic, and psychrophilic microorganisms scattered among 11 bacterial divisions. No archaea were found. The species composition of the enrichments was affected by the length of the hot periods experienced at low tide and was very different from those found in the biomass. A total of 36 chitinase genes were detected by molecular screening of the samples with degenerate primers for glycoside hydrolase family 18. The chitinase gene diversity was at least twofold higher in the enrichment samples than in the controls, indicating that a much higher diversity of hydrolytic genes can be accessed with this approach.
Assignment 3 – Extending the $ N Recognizer CAP 6105 Due : 10 / 14 / 11 11 : 59 pm

With the expansion of penand touch-based computing, new user interface prototypes may incorporate stroke gestures. Many gestures comprise multiple strokes, but building state-of-the-art multistroke gesture recognizers is nontrivial and time-consuming. Luckily, user interface prototypes often do not require state-ofthe-art recognizers that are general and maintainable, due to the simpler nature of most user interface gestures. To enable easy incorporation of multistroke recognition in user interface prototypes, we present $N, a lightweight, concise multistroke recognizer that uses only simple geometry and trigonometry. A full pseudocode listing is given as an appendix. $N is a significant extension to the $1 unistroke recognizer, which has seen quick uptake in prototypes but has key limitations. $N goes further by (1) recognizing gestures comprising multiple strokes, (2) automatically generalizing from one multistroke to all possible multistrokes using alternative stroke orders and directions, (3) recognizing one-dimensional gestures such as lines, and (4) providing bounded rotation invariance. In addition, $N uses two speed optimizations, one with start angles that saves 79.1% of comparisons and increases accuracy 1.3%. The other, which is optional, compares multistroke templates and candidates only if they have the same number of strokes, reducing comparisons further to 89.5% and increasing accuracy another 1.7%. These results are taken from our study of algebra symbols entered in situ by middle and high schoolers using a math tutor prototype, on which $N was 96.6% accurate with 15 templates.
ChakraVyuha � ( CV ) : A Sandbox Operating System Environment for Controlled Execution of Alien Code

Sharing of unknown programs creates an atmosphere of untrust and hence exacerbates the need to secure information and physical resources from any alien code. A sandbox approach to execution of such foreign code is proposed in this paper. An alien code is trusted with a set of privileges for accessing logical (e.g., callable functions and services) and physical (e.g., rate and maximum consumption amount of CPU, memory, disk space, etc.) resources via a third party authentication. During installation of any code in the sandbox environment, the associated privileges (per user basis) are stored in a secure area and enforced by the Operating System during execution. The alien code may also access resources defined by other subsystems (e.g., database), and hence, in an integrated environment the subsystem specific privileges are transferred securely to the subsystem for monitoring. A prototype version based on Linux OS code has been developed.
Ambulatory Assessment of Ankle and Foot Dynamics

Ground reaction force (GRF) measurement is important in the analysis of human body movements. The main drawback of the existing measurement systems is the restriction to a laboratory environment. This paper proposes an ambulatory system for assessing the dynamics of ankle and foot, which integrates the measurement of the GRF with the measurement of human body movement. The GRF and the center of pressure (CoP) are measured using two six-degrees-of-freedom force sensors mounted beneath the shoe. The movement of foot and lower leg is measured using three miniature inertial sensors, two rigidly attached to the shoe and one on the lower leg. The proposed system is validated using a force plate and an optical position measurement system as a reference. The results show good correspondence between both measurement systems, except for the ankle power estimation. The root mean square (RMS) difference of the magnitude of the GRF over 10 evaluated trials was (0.012 plusmn 0.001) N/N (mean plusmn standard deviation), being (1.1 plusmn 0.1)% of the maximal GRF magnitude. It should be noted that the forces, moments, and powers are normalized with respect to body weight. The CoP estimation using both methods shows good correspondence, as indicated by the RMS difference of (5.1 plusmn 0.7) mm, corresponding to (1.7 plusmn 0.3)% of the length of the shoe. The RMS difference between the magnitudes of the heel position estimates was calculated as (18 plusmn 6) mm, being (1.4 plusmn 0.5)% of the maximal magnitude. The ankle moment RMS difference was (0.004 plusmn 0.001) Nm/N, being (2.3 plusmn 0.5)% of the maximal magnitude. Finally, the RMS difference of the estimated power at the ankle was (0.02 plusmn 0.005) W/N, being (14 plusmn 5)% of the maximal power. This power difference is caused by an inaccurate estimation of the angular velocities using the optical reference measurement system, which is due to considering the foot as a single segment. The ambulatory system considers separate heel and forefoot segments, thus allowing an additional foot moment and power to be estimated. Based on the results of this research, it is concluded that the combination of the instrumented shoe and inertial sensing is a promising tool for the assessment of the dynamics of foot and ankle in an ambulatory setting