Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-homology protein threading

Motivation: The challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method HHpred. However, HHpred does not fare well when proteins under consideration are low-homology. A protein is low-homology if we cannot obtain sufficient amount of homologous information for it from existing protein sequence databases. Results: We present a profile-entropy dependent scoring function for low-homology protein threading. This method will model correlation among various protein features and determine their relative importance according to the amount of homologous information available. When proteins under consideration are low-homology, our method will rely more on structure information; otherwise, homologous information. Experimental results indicate that our threading method greatly outperforms the best profile-based method HHpred and all the top CASP8 servers on low-homology proteins. Tested on the CASP8 hard targets, our threading method is also better than all the top CASP8 servers but slightly worse than Zhang-Server. This is significant considering that Zhang-Server and other top CASP8 servers use a combination of multiple structure-prediction techniques including consensus method, multiple-template modeling, template-free modeling and model refinement while our method is a classical single-template-based threading method without any post-threading refinement. Contact: jinboxu@gmail.com
Erasure Code for Efficient Error Correction in Block Data Transmission

This paper proposes an innovative technique for correcting transmission burst errors in data transmitted over amplitude modulated channels suffering from strong electromagnetic interference, such as encountered in military situations. Efficiency is achieved by separating the error detection from the correction process and using different codes for each case. The proposed technique is based on simple mathematical operations and is suitable for implementation in FPGA devices. It is shown to be more efficient than existing ones, according to criteria that are relevant to current applications.
Efficacy of omega-3 fatty acid supplements (eicosapentaenoic acid and docosahexaenoic acid) in the secondary prevention of cardiovascular disease: a meta-analysis of randomized, double-blind, placebo-controlled trials.

BACKGROUND Although previous randomized, double-blind, placebo-controlled trials reported the efficacy of omega-3 fatty acid supplements in the secondary prevention of cardiovascular disease (CVD), the evidence remains inconclusive. Using a meta-analysis, we investigated the efficacy of eicosapentaenoic acid and docosahexaenoic acid in the secondary prevention of CVD. METHODS We searched PubMed, EMBASE, and the Cochrane Library in April 2011. Two of us independently reviewed and selected eligible randomized controlled trials. RESULTS Of 1007 articles retrieved, 14 randomized, double-blind, placebo-controlled trials (involving 20 485 patients with a history of CVD) were included in the final analyses. Supplementation with omega-3 fatty acids did not reduce the risk of overall cardiovascular events (relative risk, 0.99; 95% CI, 0.89-1.09), all-cause mortality, sudden cardiac death, myocardial infarction, congestive heart failure, or transient ischemic attack and stroke. There was a small reduction in cardiovascular death (relative risk, 0.91; 95% CI, 0.84-0.99), which disappeared when we excluded a study with major methodological problems. Furthermore, no significant preventive effect was observed in subgroup analyses by the following: country location, inland or coastal geographic area, history of CVD, concomitant medication use, type of placebo material in the trial, methodological quality of the trial, duration of treatment, dosage of eicosapentaenoic acid or docosahexaenoic acid, or use of fish oil supplementation only as treatment. CONCLUSION Our meta-analysis showed insufficient evidence of a secondary preventive effect of omega-3 fatty acid supplements against overall cardiovascular events among patients with a history of cardiovascular disease.
Shallow Medial Tibial Plateau and Steep Medial and Lateral Tibial Slopes: New Risk Factors for Anterior Cruciate Ligament Injuries

Background The geometry of the tibial plateau has been largely ignored as a source of possible risk factors for anterior cruciate ligament injury. Discovering the anterior cruciate ligament injury risk factors associated with the tibial plateau may lead to delineation of the existing sex-based disparity in anterior cruciate ligament injuries and help develop strategies for the prevention of anterior cruciate ligament injuries regardless of gender. Hypothesis Individuals with a shallower medial tibial depth of concavity, while having increased posteriorly directed slope of their tibial plateau, are at increased risk of suffering an anterior cruciate ligament injury compared with those with decreased posterior slope and increased medial tibial depth. Furthermore, these relationships are different between men and women. Study Design Case-control study (prevalence); Level of evidence, 3. Methods The medial, lateral, and coronal tibial plateau slopes as well as the medial tibial depth of concavity in 55 uninjured controls (33 women and 22 men) and 49 anterior cruciate ligament—injured cases (27 women and 22 men) were measured using magnetic resonance images. First, a preliminary t test was performed to establish any existing differences between groups. Next, a logistic regression model was developed to determine the probability of anterior cruciate ligament injury in an individual based on the measured covariates. Results The female anterior cruciate ligament—injured cases had increased lateral tibial slope (P = .03) and shallower medial tibial depth (P = .0003) compared with the uninjured controls, while male cases had increased lateral and medial tibial slope (P = .02) and shallower medial tibial depth (P = .0004) compared with controls. The logistic regression analysis and odds ratio estimates showed that medial tibial depth is an important risk factor (odds ratio = 3.03 per 1 mm decrease in its value), followed by lateral tibial slope (odds ratio = 1.17 per 1° increase in its value) in all participants. The medial tibial slope (odds ratio = 1.18 per 1° increase in its value) was a risk factor only in men. Conclusion A combination of increased posterior-directed tibial plateau slope and shallow medial tibial plateau depth could be a major risk factor in anterior cruciate ligament injury susceptibility regardless of gender. Different injury risk models may be needed for men and women as other key risk factors are identified.
Immunocytochemistry for MUC4 and MUC16 is a useful adjunct in the diagnosis of pancreatic adenocarcinoma on fine-needle aspiration cytology.

CONTEXT Diagnoses rendered as atypical/suspicious for malignancy on fine-needle aspiration (FNA) of pancreatic mass lesions range from 2% to 29% in various studies. We have identified the expression of 3 genes, MUC4, MUC16, and NGAL that are highly upregulated in pancreatic adenocarcinoma. In this study, we analyzed the expression of these markers in FNA samples to determine whether they could improve sensitivity and specificity. OBJECTIVE To evaluate the utility of MUC4, MUC16, and NGAL in the evaluation of pancreatic FNA specimens. DESIGN Records of pancreatic FNAs performed during 10 consecutive years were reviewed. Unstained sections from corresponding cell blocks were immunostained for MUC4, MUC16, and NGAL (polyclonal). Immunostaining was assessed using the H-score (range, 0-3). Any case with an H-score of >0.5 was considered positive. RESULTS Cases were classified using cytomorphologic criteria as adenocarcinoma (31 of 64; 48.4%), benign (17 of 64; 26.6%), and atypical/suspicious (16 of 64; 25%). On follow-up, all cases (100%; 31 of 31) diagnosed as carcinoma on cytology were confirmed on biopsy/resection samples or by clinical follow-up (such as unresectable disease). Of the cases diagnosed as atypical/suspicious, 69% (11 of 16) were found to be positive for adenocarcinoma and 31% (5 of 16) were benign on subsequent follow-up. Overall sensitivity and specificity, respectively, for the various markers for the detection of pancreatic adenocarcinoma were as follows: MUC4 (74% and 100%), MUC16 (62.9% and 100%), and NGAL (61.3% and 58.8%). In cases that were atypical/suspicious on cytology, expression of MUC4 and MUC16 was 100% specific for carcinoma with sensitivities of 63.6% and 66.7%, respectively. CONCLUSION Immunocytochemistry for MUC4 and MUC16 appears to be a useful adjunct in the classification of pancreatic FNA samples, especially in cases that are equivocal (atypical/suspicious) for adenocarcinoma on cytomorphologic assessment.
Wavelet‐Based 3D Compression Scheme for Interactive Visualization of Very Large Volume Data

Interactive visualization of very large volume data has been recognized as a task requiring great effort in a variety of science and engineering fields. In particular, such data usually places considerable demands on run‐time memory space. In this paper, we present an effective 3D compression scheme for interactive visualization of very large volume data, that exploits the power of wavelet theory. In designing our method, we have compromised between two important factors: high compression ratio and fast run‐time random access ability. Our experimental results on the Visual Human data sets show that our method achieves fairly good compression ratios. In addition, it minimizes the overhead caused during run‐time reconstruction of voxel values. This 3D compression scheme will be useful in developing many interactive visualization systems for huge volume data, especially when they are based on personal computers or workstations with limited memory.
Free-Breathing Pediatric Imaging with Nonrigid Motion Correction and Parallel Imaging

PURPOSE: MR is a compelling imaging modality for children, free of risks of ionizing radiation of CT and nuclear scintigraphy studies. However, motion corrupts MR images, so children often undergo deep anesthesia and periods of suspended respiration, particularly for body MR exams. This prolongs studies and has its risks. Leveraging recent advancements in accelerated imaging and motion correction, we developed a novel method aimed to eliminate the need for deep anesthesia and breath-holds via a high-resolution motion-free volumetric MR scan acquired free-breathing with contrast-enhancement.
Identification of Novel Mutations in STAR Gene in Patients with Lipoid Congenital Adrenal Hyperplasia: A First Report from India

Lipoid congenital adrenal hyperplasia (LCAH), a rare disorder of steroid biosynthesis, is the most severe form of CAH. We report novel molecular findings of three unrelated infants with LCAH diagnosed at our center. A known missense mutation c.653C>T (p.A218V) and two novel mutations [premature termination c.441G>A (or p.W147X) and frameshift deletion c.del815G (or p.R272PfsX35)] were identified after complete sequencing of the STAR gene. Prenatal diagnosis was carried out for the family with mutation c.815delG by molecular testing wherein the fetus was found to be homozygous for the mutation. This is the first report of molecular diagnosis and prenatal testing for LCAH from India. Conflict of interest:None declared.
On the isomorphism problem of Coxeter groups and related topics = コクセター群の同型問題及び関連する話題について

At the conference the author gives a talk which surveys the definition, history and preceding results on the isomorphism problem of Coxeter groups (problem of deciding which Coxeter groups are isomorphic), together with backgrounds for Coxeter groups, applications of this problem and some related topics in the theory of Coxeter groups, including the author’s recent works. The author would like to express his gratitude to the conference organizers for giving the opportunity.
Fixed Relays for Cost Efficient 4G Network Deployments: An Evaluation

The paper provides a qualitative performance assessment of relay based deployment concepts in comparison to single-hop deployment. The results in this paper prove the general assumption that the deployment of relay nodes (RNs) provide a strong opportunity to reduce the network deployment cost substantially. It is shown how low power RNs have to be applied in cellular scenarios with high power base stations (BSs) and what cost benefits can be expected. The qualitative results show that the low power relays do have the potential to decrease the deployment cost. It is further shown that a parallelization of the relay link between the RNs and the serving BS will help to improve the cost efficiency of the relay based deployment concept.
Are the infrared-faint radio sources pulsars?

Infrared-faint radio sources (IFRS) are objects which are strong at radio wavelengths but undetected in sensitive Spitzer observations at infrared wavelengths. Their nature is uncertain and most have not yet been associated with any known astrophysical object. One possibility is that they are radio pulsars. To test this hypothesis we undertook observations of 16 of these sources with the Parkes Radio Telescope. Our results limit the radio emission to a pulsed flux density of less than 0.21 mJy (assuming a 50 per cent duty cycle). This is well below the flux density of the IFRS. We therefore conclude that these IFRS are not radio pulsars.
HUMAN-ROBOT INTERACTION BASED ON SPOKEN NATURAL LANGUAGE DIALOGUE

We report on recent work on human-robot spoken dialogue interaction in the context of Hygeiorobot, a project that aims to build a mobile robotic assistant for hospitals. Spoken dialogue systems are particularly suitable to this context, as the robot does not carry a keyboard or other common interaction devices, and is intended to be used by people with little or no computing experience. In this paper, we concentrate on dialogue management issues. After providing a brief survey of dialogue management techniques, we focus on particular issues that need to be addressed in human-robot interaction, and the considerations that influenced the design of Hygeiorobot’s dialogue manager. We then describe in detail the spoken dialogue capabilities of Hygeiorobot’s current demonstrator and the tasks that the demonstrator can perform, concluding with plans for future work.
Kinetic maintenance of context-sensitive hierarchical representations for disjoint simple polygons

We describe how to construct and kinetically maintain a tessellation of the free space between a collection of <i>k</i> disjoint simple polygonal objects with a total of <i>N</i> vertices, <i>R</i> of which are reflex. Our linear size tessellation consists of pseudo-triangles and has the following properties: (<i>i</i>) it contains disjoint outer hierarchical representations of all objects where the size of the outer boundary of these representations is proportional to a minimum link separator for the objects, and (<i>ii</i>) any line segment in the free space intersects at most <i>O</i>((<i>k</i> + log <i>R</i>) log <i>N</i>) pseudo-triangles (each of constant size). We maintain our tessellation by using the Kinetic Data Structure (KDS) framework. Our structure is compact, maintaining an active set of certificates whose number is linear in the size of a minimum link subdivision for the objects. It is also responsive; on the failure of a certificate invariants can be restored in time logarithmic in the total number of vertices. While its efficiency is difficult to establish precisely, it is shown that at most <i>O</i>(<i>k</i> + κ<inf>max</inf>log <i>R</i>)log <i>N</i> events happen during straight line motion of one object <i>A</i> in the context of <i>k</i> (fixed) others, where κ<inf>max</inf> denotes the maximum size of the minimum link polygon separating object <i>A</i> from the rest, during the motion.Furthermore, ray shooting queries (that use point location) can be answered in <i>O</i>((<i>k</i> + log <i>R</i>) log <i>N</i>) time for rays with arbitrary direction.
Association of sex work with reduced activation of the mucosal immune system.

BACKGROUND Unprotected intercourse and seminal discharge are powerful activators of the mucosal immune system and are important risk factors for transmission of human immunodeficiency virus (HIV). This study was designed to determine if female sex work is associated with changes in the mucosal immunity. METHODS Cervicovaginal lavage and plasma from 122 HIV-uninfected female sex workers (FSW) and 44 HIV-uninfected low-risk non-FSW from the same socioeconomic district of Nairobi were analyzed for evidence of immune activation (IA). The cervico-mononuclear cells (CMC) were analyzed for cellular activation by flow cytometry. RESULTS Lower IA was observed in FSW compared to the low-risk women as demonstrated by the lower level of MIP-3α (P < .001), ITAC (P < .001), MIG (p.0001), IL-1α (P < .001), IL-1β (P < .001), IL-1Rα (P = .0002), IL-6 (P < .001), IL-8 (P < .001), IL-10 (P = .01), IP-10 (P = .0001), MDC (P < .001), MIP-1α, (P < .001), MIP-1β (P = .005), MCP-1 (P = .03), and TNF-α (P = .006). Significant differences were noted as early as 1 year following initiation of sex work and increased with duration of sex work. CONCLUSION This study showed that sex work is associated with important changes in the mucosal immune system. By analyzing chemokine/cytokine levels and CMC activation, we observed a lower mucosal IA in HIV-uninfected FSW compared to low-risk women.
Cold Storage in the Cloud : Trends , Challenges , and Solutions

Current usage models include backup, disaster recovery, archiving, and social media. Though each usage model has distinct characteristics, they all share requirements for adequate storage performance, availability, data integrity, and security. Additionally, compatibility with existing enterprise architecture is important for seamless access to data as well as to simplify manageability, which helps reduce total cost of ownership (TCO). 1
Laser ranging and video imaging for bin picking Faysal

This paper describes an imaging system that was developed to aid industrial bin picking tasks. The purpose of this system was to provide accurate 3D models of parts and objects in the bin, so that precise grasping operations could be performed. The technology described here is based on two types of sensors: range mapping scanners and video cameras. The geometry of bin contents was reconstructed from range maps and modeled using superquadric representations, providing location and parts surface information that can be employed to guide the robotic arm. Texture was also provided by the video streams and applied to the recovered models. The system is expected to improve the accuracy and efficiency of bin sorting and represents a step toward full automation.
Supporting Group Decision Making and Coordination in Urban Disasters Relief

When extreme events affect urban areas the response process should be fast and effective because the population and civil infrastructure densities potentially increase the impact of such events. These situations have shown the need to improve the group decisionmaking process and the coordination of relief activities carried out by relief organizations. This paper proposes to include first responders as decision makers and describes a technological platform to support decision making and coordination activities among these all actors involved. The supporting platform provides digital communication and information recording, representation and dissemination capabilities among the mobile workers participating in the relief efforts. The platform could also be used to support activities in scenarios similar to this one (e.g. police and military operations, massive social events).
Departement Elektrotechniek ESAT-SISTA / TR 2003-169 Adaptive Bitrate Maximizing TEQ Design for DMT-based Systems 1

In a previous paper, we proposed a bitrate maximizing (BM) design criterion for the time-domain equalizer (TEQ) in a discrete multitone receiver. This BM-TEQ and the closely related BM per-group equalizers (PGEQ) get close to the performance of the so-called per-tone equalization (PTEQ). In this paper, we show that the BM-TEQ criterion, despite its nonlinear nature, is well suited for a recursive Levenberg-Marquardt (RLM) based design. This adaptive BM-TEQ also allows to track slow variations of the transmission channel and the noise. This RLM-based design uses the same second-order statistics (SOS) as the earlier presented recursive least-squares (RLS) based adaptive PTEQ and opens up a complete range of adaptive BM equalizers: from the computationally efficient RLS-based PTEQ with largest memory cost, over the RLM-based BM-PGEQ with intermediate memory cost, towards an RLM-based BM-TEQ with considerably smaller memory cost, but larger equalizer updating complexity.
The Class A Macrophage Scavenger Receptor Attenuates CXC Chemokine Production and the Early Infiltration of Neutrophils in Sterile Peritonitis1

The macrophage scavenger receptor (SR-A) is a multifunctional receptor that is associated with several important pathological conditions, including atherosclerosis. In this study, we show, using a sterile peritonitis model, that it can regulate the inflammatory response. SR-A null mice display an increased initial granulocytic infiltration because of overproduction of the CXC chemokines, MIP-2 and keratinocyte-derived cytokine. This differential response is dependent upon particle internalization and can be mimicked by advanced glycation end product-BSA-conjugated latex beads. Thus SR-A is a nonactivating receptor, which is the first example of a pattern recognition receptor that serves to counter the activities of proinflammatory receptors and attenuates the production of specific chemokines to ensure an inflammatory response of the appropriate magnitude.
A combination of the IPAG questionnaire and PiKo-6® flow meter is a valuable screening tool for COPD in the primary care setting.

AIMS To investigate the validity of the International Primary Care Airways Guidelines (IPAG) questionnaire and PiKo-6® (Ferraris Respiratory Europe Ltd.) flow meter as screening tools for diagnosing chronic obstructive pulmonary disease (COPD) in the primary care setting. METHODS The first 50 patients in 25 general practice offices completed the IPAG questionnaire and underwent spirometry with the handheld PiKo-6® flow meter. The results were compared with official spirometry parameters after bronchodilation. All participants had no previous medical diagnosis of respiratory diseases. RESULTS Data from 1,078 out of 1,250 subjects (462 males, mean age 65.3 ± 11.4 years) were analysed. The percentage of smokers was 48.4% (38 ± 29 pack-years). COPD was diagnosed in 111 (10.3%) patients. In the subgroup of smokers the sensitivity and specificity for COPD diagnosis were 91% and 49%, respectively, for the IPAG questionnaire; 80% and 95% respectively for the PiKo-6® spirometer; and 72% and 97% for their combination. The negative predictive value of the questionnaire was 97%, whereas the positive predictive value of the questionnaire/ PiKo-6® combination was 82%. Using a cut-off score of 19 points for the IPAG questionnaire, we calculated the best combination of sensitivity (75%) and specificity (72%). CONCLUSIONS The IPAG questionnaire and the hand-held PiKo-6® spirometer can be used in combination to increase the possibility of an early and accurate diagnosis of COPD in the primary care setting.