Miracle-dz/UniFAR-FTUs huggingface dataset:
Glycemic Control after Total Pancreatectomy for Intraductal Papillary Mucinous Neoplasm: An Exploratory Study

Background. Glycemic control following total pancreatectomy (TP) has been thought to be difficult to manage. Diffuse intraductal papillary mucinous neoplasm (IPMN) is a potentially curable precursor to pancreatic adenocarcinoma, best treated by TP. Objective. Compare glycemic control in patients undergoing TP for IPMN to patients with type 1 diabetes mellitus (DM). Design/Setting. Retrospective cohort. Outcome Measure. Hemoglobin A1C(HbA1C) at 6, 12, 18, and 24 months after TP. In the control group, baseline was defined as 6 months prior to the first HbA1c measure. Results. Mean HgbA1C at each point of interest was similar between TP and type I DM patients (6 months (7.5% versus 7.7%, P = 0.52), 12 months (7.3% versus 8.0%, P = 0.081), 18 months (7.7% and 7.6%, P = 0.64), and at 24 months (7.3% versus 7.8%, P = 0.10)). Seven TP patients (50%) experienced a hypoglycemic event compared to 65 type 1 DM patients (65%, P = 0.38). Limitations. Small number of TP patients, retrospective design, lack of long-termfollowup. Conclusion. This suggests that glycemic control following TP for IPMNcan be well managed, similar to type 1 DM patients. Fear of DM following TP for IPMN should not preclude surgery when TP is indicated.
Is SC+ILP=RC?

Sequential consistency (SC) is the simplest programming interface for shared-memory systems but imposes program order among all memory operations, possibly precluding high performance implementations. Release consistency (RC), however, enables the highest performance implementations but puts the burden on the programmer to specify which memory operations need to be atomic and in program order. This paper shows, for the first time, that SC implementations can perform as well as RC implementations if the hardware provides enough support for speculation. Both SC and RC implementations rely on reordering and overlapping memory operations for high performance. To enforce order when necessary, an RC implementation uses software guarantees, whereas an SC implementation relies on hardware speculation. Our SC implementation, called SC++, closes the performance gap because: (1) the hardware allows not just loads, as some current SC implementations do, but also stores to bypass each other speculatively to hide remote latencies, (2) the hardware provides large speculative state for not just processor, as previously proposed, but also memory to allow out-of-order memory operations, (3) the support for hardware speculation does not add excessive overheads to processor pipeline critical paths, and (4) well-behaved applications incur infrequent rollbacks of speculative execution. Using simulation, we show that SC++ achieves an RC implementation's performance in all the six applications we studied.
Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction

An emulsion-based serial crystallographic technology has been developed, in which single crystals are grown in nanolitre-sized droplets inside an X-ray semi-transparent microfluidic chip exploiting a negative feedback mechanism. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored in the chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals to solve the structure of glucose isomerase to 2.1 Å.
Mycobacterial Gene Cloning and Expression, Comparative Genomics, Bioinformatics and Proteomics in Relation to the Development of New Vaccines and Diagnostic Reagents

Recent advances in molecular and genomic techniques have facilitated research on several aspects of mycobacteriology, such as diagnosis and the identification of new vaccines and therapeutic targets for various diseases, including tuberculosis. The aim of this review was to analyze the implications of advances in molecular and genomic techniques on the development of new vaccines for tuberculosis as well as immunological reagents to diagnose the disease. Gene cloning and expression, DNA and protein sequencing, polymerase chain reaction, comparative genomics, bioinformatics, proteomics and DNA and peptide synthesis coupled with the application of cellular immunology techniques have led to the identification of several antigens of Mycobacterium tuberculosis, which have potential for diagnosis and vaccine applications. For example, cross-reactive mycobacterial antigens like heat shock proteins, MTB32 and MTB39, have been identified as new vaccine candidates, and antigens encoded by M. tuberculosis-specific genomic regions as new reagents for diagnosis.
Time series data mining in systems biology

Analysis of time series data constitutes an important activity in many scientific disciplines. Over the last years there has been an increase in the collection of time series data in all scientific fields and disciplines, such as the industry and engineering. Due to the increasing size of the time series datasets, new automated time series data mining techniques have been devised for comparing time series data and present information in a logical and easily comprehensible structure.In systems biology in particular, time series are used to the study biological systems. The time series representations of a systems? dynamics behaviour are multivariate time series. Time series are considered multivariate when they contain observations for more than one variable component. The biological systems? dynamics time series contain observations for every feature component that is included in the system; they thus are multivariate time series. Recently, there has been an increasing interest in the collection of biological time series. It would therefore be beneficial for systems biologist to be able to compare these multivariate time series.Over the last decade, the field of time series analysis has attracted the attention of people from different scientific disciplines. A number of researchers from the data mining community focus their efforts on providing solutions on numerous problems regarding different time series data mining tasks. Different methods have been proposed for instance, for comparing, indexing and clustering, of univariate time series. Furthermore, different methods have been proposed for creating abstract representations of time series data and investigating the benefits of using these representations for data mining tasks.The introduction of more advanced computing resources facilitated the collection of multivariate time series, which has become common practise in various scientific fields. The increasing number of multivariate time series data triggered the demand for methods to compare them. A small number of well-suited methods have been proposed for comparing these multivariate time series data.All the currently available methods for multivariate time series comparison are more than adequate for comparing multivariate time series with the same dimensionality. However, they all suffer the same drawback. Current techniques cannot process multivariate time series with different dimensions. A proposed solution for comparing multivariate time series with arbitrary dimensions requires the creation of weighted averages. However, the accumulation of weights data is not always feasible.In this project, a new method is proposed which enables the comparison of multivariate time series with arbitrary dimensions. The particular method is evaluated on multivariate time series from different disciplines in order to test the methods? applicability on data from different fields of science and industry. Lastly, the newly formed method is applied to perform different time series data mining analyses on a set of biological data.
Multiple testing in genome-wide association studies via hidden Markov models

MOTIVATION Genome-wide association studies (GWAS) interrogate common genetic variation across the entire human genome in an unbiased manner and hold promise in identifying genetic variants with moderate or weak effect sizes. However, conventional testing procedures, which are mostly P-value based, ignore the dependency and therefore suffer from loss of efficiency. The goal of this article is to exploit the dependency information among adjacent single nucleotide polymorphisms (SNPs) to improve the screening efficiency in GWAS. RESULTS We propose to model the linear block dependency in the SNP data using hidden Markov models (HMMs). A compound decision-theoretic framework for testing HMM-dependent hypotheses is developed. We propose a powerful data-driven procedure [pooled local index of significance (PLIS)] that controls the false discovery rate (FDR) at the nominal level. PLIS is shown to be optimal in the sense that it has the smallest false negative rate (FNR) among all valid FDR procedures. By re-ranking significance for all SNPs with dependency considered, PLIS gains higher power than conventional P-value based methods. Simulation results demonstrate that PLIS dominates conventional FDR procedures in detecting disease-associated SNPs. Our method is applied to analysis of the SNP data from a GWAS of type 1 diabetes. Compared with the Benjamini-Hochberg (BH) procedure, PLIS yields more accurate results and has better reproducibility of findings. CONCLUSION The genomic rankings based on our procedure are substantially different from the rankings based on the P-values. By integrating information from adjacent locations, the PLIS rankings benefit from the increased signal-to-noise ratio, hence our procedure often has higher statistical power and better reproducibility. It provides a promising direction in large-scale GWAS. AVAILABILITY An R package PLIS has been developed to implement the PLIS procedure. Source codes are available upon request and will be available on CRAN (http://cran.r-project.org/). CONTACT zhiwei@njit.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Thirty-year trends in sudden deafness from four nationwide epidemiological surveys in Japan

Conclusions. The estimated annual number of patients with sudden deafness treated in Japan has increased during the last 30 years, especially in the elderly population. Hypertension and diabetes mellitus could contribute to the etiology of this disorder. Objectives. To investigate the epidemiological trends of sudden deafness in Japan over the past 30 years by analyzing data from national surveys. Materials and methods. Nationwide epidemiological surveys on sudden deafness were conducted four times by the Research Committee of the Ministry of Health and Welfare in Japan. The first, second, third, and fourth surveys were performed in 1972, 1987, 1993, and 2001, respectively. Results. The estimated annual numbers of patients with sudden deafness treated in Japan were 4000 in 1972; 16 700 in 1987; 24 000 in 1993, and 35 000 in 2001.The average ages of patients at onset were 39.1, 45.4, 49.3, and 51.3 years, respectively. Thus, both the number of patients and the average age of patients with sudden deafness have increased during the past 30 years. Patients with sudden deafness in the fourth survey exhibited hypertension and diabetes mellitus more frequently than did patients in the first survey; this trend was particularly noticeable among elderly patients.
Rapid Maturation of Effector T Cells in Tumors, but Not Lymphoid Organs, during Tumor Regression

Increasing the efficacy of adoptively transferred, tumor antigen specific T cells is a major goal of immunotherapy. Clearly, a more thorough understanding of the effector phase of T cell responses, within the tumor site itself, would be beneficial. To examine this issue, we adoptively transferred tumor antigen-specific effector T cells into tumor-bearing mice, then performed kinetic evaluations of their phenotype, function, and survival in tumors, draining lymph nodes (dLNs), and spleens during regression of murine fibrosarcomas. Effector function in tumors was quantitated through the use of a novel intratumoral cytolytic assay. This approach revealed dynamic changes in the phenotype, cytolytic capacity, and viability of tumor infiltrating effector T cells during the course of tumor regression. Over a period of days, T cells within tumors rapidly transitioned from a CD25hi/CD27hi to a CD25low/CD27low phenotype and displayed an increase in cytolytic capacity, indicative of effector maturation. Simultaneously, however, the viability of maturing T cells within tumors diminished. In contrast, transferred T cells trafficking through lymphoid organs were much more static, as they maintained a stable phenotype, robust cytolytic activity, and high viability. Therefore, there exists a marked phenotypic and functional divergence between tumor-infiltrating effector T cells and their counterparts in lymphoid organs. Our results indicate that the population of tumor-infiltrating T cells is unique in experiencing rapid effector maturation post-transfer, and suggest that strategies aimed at prolonging the survival of CD25low/CD27low full effectors, which displayed the highest levels of intratumoral cytolytic activity, should enhance the efficacy of T cell based tumor immunotherapies.
Computational Insights on Sulfonamide Imprinted Polymers

Molecular imprinting is one of the most efficient methods for preparing synthetic receptors that possess user defined recognition properties. Despite general success of non-covalent imprinting for a large variety of templates, some groups of compounds remain difficult to tackle due to their structural complexity. In this study we investigate preparation of molecularly imprinted polymers that can bind sulfonamide compounds, which represent important drug candidates. Compared to the biological system that utilizes metal coordinated interaction, the imprinted polymer provided pronounced selectivity when hydrogen bond interaction was employed in an organic solvent. Computer simulation of the interaction between the sulfonamide template and functional monomers pointed out that although methacrylic acid had strong interaction energy with the template, it also possessed high non-specific interaction with the solvent molecules of tetrahydrofuran as well as being prone to self-complexation. On the other hand, 1-vinyl-imidazole was suitable for imprinting sulfonamides as it did not cross-react with the solvent molecules or engage in self-complexation structures.
A Perceptual Matching Technique for Depth Judgments in Optical, See-Through Augmented Reality

A fundamental problem in optical, see-through augmented reality (AR) is characterizing how it affects the perception of spatial layout and depth. This problem is important because AR system developers need to both place graphics in arbitrary spatial relationships with real-world objects, and to know that users will perceive them in the same relationships. Furthermore, AR makes possible enhanced perceptual techniques that have no real-world equivalent, such as x-ray vision, where AR users are supposed to perceive graphics as being located behind opaque surfaces. This paper reviews and discusses techniques for measuring egocentric depth judgments in both virtual and augmented environments. It then describes a perceptual matching task and experimental design for measuring egocentric AR depth judgments at medium- and far-field distances of 5 to 45 meters. The experiment studied the effect of field of view, the x-ray vision condition, multiple distances, and practice on the task. The paper relates some of the findings to the well-known problem of depth underestimation in virtual environments, and further reports evidence for a switch in bias, from underestimating to overestimating the distance of AR-presented graphics, at 23 meters. It also gives a quantification of how much more difficult the x-ray vision condition makes the task, and then concludes with ideas for improving the experimental methodology.
Signaling from Smo to Ci/Gli: conservation and divergence of Hedgehog pathways from Drosophila to vertebrates

Although the framework of the Hedgehog (Hh) signaling pathway is evolutionarily conserved, recent studies indicate that fundamental differences exist between Drosophila and vertebrates in the way signals are transduced from the membrane protein Smoothened (Smo) to the Ci/Gli transcription factors. For example, Smo structure and the roles of fused and Suppressor of fused have diverged. Recently, many vertebrate-specific components have been identified that act between Smo and Gli. These include intraflagellar transport proteins, which link vertebrate Hh signaling to cilia. Because abnormal Hh signaling can cause birth defects and cancer, these vertebrate-specific components may have roles in human health.
Diversity in obscurity: fossil flowers and the early history of angiosperms

In the second half of the nineteenth century, pioneering discoveries of rich assemblages of fossil plants from the Cretaceous resulted in considerable interest in the first appearance of angiosperms in the geological record. Darwin's famous comment, which labelled the ‘rapid development’ of angiosperms an ‘abominable mystery’, dates from this time. Darwin and his contemporaries were puzzled by the relatively late, seemingly sudden and geographically widespread appearance of modern-looking angiosperms in Late Cretaceous floras. Today, the early diversification of angiosperms seems much less ‘rapid’. Angiosperms were clearly present in the Early Cretaceous, 20–30 Myr before they attained the level of ecological dominance reflected in some mid-Cretaceous floras, and angiosperm leaves and pollen show a distinct pattern of steadily increasing diversity and complexity through this interval. Early angiosperm fossil flowers show a similar orderly diversification and also provide detailed insights into the changing reproductive biology and phylogenetic diversity of angiosperms from the Early Cretaceous. In addition, newly discovered fossil flowers indicate considerable, previously unrecognized, cryptic diversity among the earliest angiosperms known from the fossil record. Lineages that today have an herbaceous or shrubby habit were well represented. Monocotyledons, which have previously been difficult to recognize among assemblages of early fossil angiosperms, were also diverse and prominent in many Early Cretaceous ecosystems.
Forecasting the Future of Stroke in the United States: A Policy Statement From the American Heart Association and American Stroke Association

Background and Purpose— Stroke is a leading cause of disability, cognitive impairment, and death in the United States and accounts for 1.7% of national health expenditures. Because the population is aging and the risk of stroke more than doubles for each successive decade after the age of 55 years, these costs are anticipated to rise dramatically. The objective of this report was to project future annual costs of care for stroke from 2012 to 2030 and discuss potential cost reduction strategies. Methods and Results— The American Heart Association/American Stroke Association developed methodology to project the future costs of stroke-related care. Estimates excluded costs associated with other cardiovascular diseases (hypertension, coronary heart disease, and congestive heart failure). By 2030, 3.88% of the US population >18 years of age is projected to have had a stroke. Between 2012 and 2030, real (2010$) total direct annual stroke-related medical costs are expected to increase from $71.55 billion to $184.13 billion. Real indirect annual costs (attributable to lost productivity) are projected to rise from $33.65 billion to $56.54 billion over the same period. Overall, total annual costs of stroke are projected to increase to $240.67 billion by 2030, an increase of 129%. Conclusions— These projections suggest that the annual costs of stroke will increase substantially over the next 2 decades. Greater emphasis on implementing effective preventive, acute care, and rehabilitative services will have both medical and societal benefits. (Stroke. 2013;44:2361-2375.)
Two UV-Sensitive Photoreceptor Proteins, Opn5m and Opn5m2 in Ray-Finned Fish with Distinct Molecular Properties and Broad Distribution in the Retina and Brain

Opn5 is a group within the opsin family of proteins that is responsible for visual and non-visual photoreception in animals. It consists of several subgroups, including Opn5m, the only subgroup containing members found in most vertebrates, including mammals. In addition, recent genomic information has revealed that some ray-finned fishes carry paralogous genes of Opn5m while other fishes have no such genes. Here, we report the molecular properties of the opsin now called Opn5m2 and its distributions in both the retina and brain. Like Opn5m, Opn5m2 exhibits UV light-sensitivity when binding to 11-cis-retinal and forms a stable active state that couples with Gi subtype of G protein. However, Opn5m2 does not bind all-trans-retinal and exhibits exclusive binding to 11-cis-retinal, whereas many bistable opsins, including fish Opn5m, can bind directly to all-trans-retinal as well as 11-cis-retinal. Because medaka fish has lost the Opn5m2 gene from its genome, we compared the tissue distribution patterns of Opn5m in medaka fish, zebrafish, and spotted gar, in addition to the distribution patterns of Opn5m2 in zebrafish and spotted gar. Opn5m expression levels showed a gradient along the dorsal–ventral axis of the retina, and preferential expression was observed in the ventral retina in the three fishes. The levels of Opn5m2 showed a similar gradient with preferential expression observed in the dorsal retina. Opn5m expression was relatively abundant in the inner region of the inner nuclear layer, while Opn5m2 was expressed in the outer edge of the inner nuclear layer. Additionally, we could detect Opn5m expression in several brain regions, including the hypothalamus, of these fish species. Opn5m2 expression could not be detected in zebrafish brain, but was clearly observed in limited brain regions of spotted gar. These results suggest that ray-finned fishes can generally utilize UV light information for non-image-forming photoreception in a wide range of cells in the retina and brain.
3D Marking menu selection with freehand gestures

A controlled experiment was performed to evaluate the usability of freehand gestural target selection with different 3D marking menu layouts and target directions. We found that a rectangular layout was faster than an octagonal layout, with no significant increase in errors, and that our right-handed participants preferred to select to the right and forwards in a 3D marking menu. We propose an improved design for 3D marking menus based on our findings. The experimental results also suggest that designers should consider carefully whether or not findings from similar interaction techniques using hands-on devices can be carried over to the design of freehand gestural interaction.
Combined Effects of Total Ionizing Dose and Temperature on a K-Band Quadrature LC-Tank VCO in a 32 nm CMOS SOI Technology

A 20.4 GHz VCO with a tuning range of 610 MHz (3%) was designed and fabricated in a 32 nm CMOS silicon-on-insulator technology. At 36 °C, the VCO achieves an output power of 0.1 dBm and a phase noise of −99 dBc/Hz at 1 MHz offset from the center frequency. TID experiments on the VCO operating at 36 °C, 75 °C, and 100 °C show degradation in frequency, output power, and phase noise. At 100 °C and 500 krad(SiO2), the VCO shows a worst-case degradation of 630 MHz, 4.3 dBm, and 6.1 dBc/Hz in center frequency, output power, and phase noise, respectively. At 36 °C and up to 500 krad(SiO2), the VCO can be retuned to operate at the required center frequency of 20.4 GHz. However, at 100 °C, the combined effects of temperature and TID result in specification failure. The system-level impact of TID-induced degradation on VCO performance is discussed using a phase-locked loop (PLL) as an example application. Measured performance corroborates previous predictions and highlights the importance of combined effects testing for advanced RF design characterization and qualification.