Miracle-dz/UniFAR-FTUs huggingface dataset:
Hemispherical Harmonic Surface Description and Applications to Medical Image Analysis

The use of surface harmonics for rigid and nonrigid shape description is well known. In this paper we define a set of complete hemispherical harmonic basis functions on a hemisphere domain and propose a novel parametric shape description method to efficiently and flexibly represent the surfaces of anatomical structures in medical images. As the first application of hemispherical harmonic theory in shape description, our technique differs from the previous surface harmonics shape descriptors, all of which don't work efficiently on the hemisphere-like objects that often exist in medical anatomical structures (e.g., ventricles, atriums, etc.). We demonstrate the effectiveness of our approach through theoretic and experimental exploration of a set of medical image applications. Furthermore, an evaluation criterion for surface modeling efficiency is described and the comparison results demonstrated that our method outperformed the previous approaches using spherical harmonic models.
Exhaled volatile organic compounds discriminate patients with chronic obstructive pulmonary disease from healthy subjects

Chronic obstructive pulmonary disease (COPD) is a chronic airway inflammatory disease characterized by incompletely reversible airway obstruction. This clinically heterogeneous group of patients is characterized by different phenotypes. Spirometry and clinical parameters, such as severity of dyspnea and exacerbation frequency, are used to diagnose and assess the severity of COPD. The purpose of this study was to investigate whether volatile organic compounds (VOCs) could be detected in the exhaled breath of patients with COPD and whether these VOCs could distinguish COPD patients from healthy subjects. Moreover, we aimed to investigate whether VOCs could be used as biomarkers for classifying patients into different subgroups of the disease. Ion mobility spectrometry was used to detect VOCs in the exhaled breath of COPD patients. One hundred and thirty-seven peaks were found to have a statistically significant difference between the COPD group and the combined healthy smokers and nonsmoker group. Six of these VOCs were found to correctly discriminate COPD patients from healthy controls with an accuracy of 70%. Only 15 peaks were found to be statistically different between healthy smokers and healthy nonsmokers. Furthermore, by determining the cutoff levels for each VOC peak, it was possible to classify the COPD patients into breathprint subgroups. Forced expiratory volume in 1 second, body mass index, and C-reactive protein seem to play a role in the discrepancies observed in the different breathprint subgroups.
Anaerobic oxidation of methane by sulfate in hypersaline groundwater of the Dead Sea aquifer

Geochemical and microbial evidence points to anaerobic oxidation of methane (AOM) likely coupled with bacterial sulfate reduction in the hypersaline groundwater of the Dead Sea (DS) alluvial aquifer. Groundwater was sampled from nine boreholes drilled along the Arugot alluvial fan next to the DS. The groundwater samples were highly saline (up to 6300 mm chlorine), anoxic, and contained methane. A mass balance calculation demonstrates that the very low δ13CDIC in this groundwater is due to anaerobic methane oxidation. Sulfate depletion coincident with isotope enrichment of sulfur and oxygen isotopes in the sulfate suggests that sulfate reduction is associated with this AOM. DNA extraction and 16S amplicon sequencing were used to explore the microbial community present and were found to be microbial composition indicative of bacterial sulfate reducers associated with anaerobic methanotrophic archaea (ANME) driving AOM. The net sulfate reduction seems to be primarily controlled by the salinity and the available methane and is substantially lower as salinity increases (2.5 mm sulfate removal at 3000 mm chlorine but only 0.5 mm sulfate removal at 6300 mm chlorine). Low overall sulfur isotope fractionation observed (34ε = 17 ± 3.5‰) hints at high rates of sulfate reduction, as has been previously suggested for sulfate reduction coupled with methane oxidation. The new results demonstrate the presence of sulfate‐driven AOM in terrestrial hypersaline systems and expand our understanding of how microbial life is sustained under the challenging conditions of an extremely hypersaline environment.
DESIGNING QUESTIONNAIRES FOR USE IN MULTICULTURAL CONTEXTS

Measurement is an integral part of the assessment process in social work. Whether or not this is done formally, social workers inevitably quantify the functioning of client systems during assessment: “This community lacks access to social resources; this family experiences high levels of conflict; this person has a severe drug addiction. ” All of these statements, typical of social work assessments, involve measurement.
GTP Hydrolysis of TC10 Promotes Neurite Outgrowth through Exocytic Fusion of Rab11- and L1-Containing Vesicles by Releasing Exocyst Component Exo70

The use of exocytosis for membrane expansion at nerve growth cones is critical for neurite outgrowth. TC10 is a Rho family GTPase that is essential for specific types of vesicular trafficking to the plasma membrane. Recent studies have shown that TC10 and its effector Exo70, a component of the exocyst tethering complex, contribute to neurite outgrowth. However, the molecular mechanisms of the neuritogenesis-promoting functions of TC10 remain to be established. Here, we propose that GTP hydrolysis of vesicular TC10 near the plasma membrane promotes neurite outgrowth by accelerating vesicle fusion by releasing Exo70. Using Förster resonance energy transfer (FRET)-based biosensors, we show that TC10 activity at the plasma membrane decreased at extending growth cones in hippocampal neurons and nerve growth factor (NGF)-treated PC12 cells. In neuronal cells, TC10 activity at vesicles was higher than its activity at the plasma membrane, and TC10-positive vesicles were found to fuse to the plasma membrane in NGF-treated PC12 cells. Therefore, activity of TC10 at vesicles is presumed to be inactivated near the plasma membrane during neuronal exocytosis. Our model is supported by functional evidence that constitutively active TC10 could not rescue decrease in NGF-induced neurite outgrowth induced by TC10 depletion. Furthermore, TC10 knockdown experiments and colocalization analyses confirmed the involvement of Exo70 in TC10-mediated trafficking in neuronal cells. TC10 frequently resided on vesicles containing Rab11, which is a key regulator of recycling pathways and implicated in neurite outgrowth. In growth cones, most of the vesicles containing the cell adhesion molecule L1 had TC10. Exocytosis of Rab11- and L1-positive vesicles may play a central role in TC10-mediated neurite outgrowth. The combination of this study and our previous work on the role of TC10 in EGF-induced exocytosis in HeLa cells suggests that the signaling machinery containing TC10 proposed here may be broadly used for exocytosis.
A heuristic model for scheduling wind turbines

Due to variability of electricity price, grid demand and wind speed as well as heterogeneity of wind turbines, operators of a wind farm encounter challenges of determining operational status of wind turbines (on/off) to achieve power generation objectives but minimize the total cost. A heuristic model that develops scheduling strategies of wind turbines for operators in a wind farm is discussed in this paper. A modified particle swarm optimization algorithm with small world network structure is introduced to solve the heuristic model. The computed scheduling strategies suggest the operational status of wind turbines over the pre-determined scheduling horizon that minimizes the total cost of a wind farm.
Ant Colony Optimization for optimal path finding in protein interaction network

Recently, we have proposed ant colony optimization (ACO) algorithm together with traveling salesman problem (TSP) approach to cluster proteins in protein interaction network (PIN). Our proposal described the general adaptation of ACO to perform the clustering tasks, including the optimal path finding in PIN. In this paper, we focus precisely on the process of finding an optimal path by ACO for the given PIN.
Comparative Readability Analysis of Online Patient Education Resources on Inflammatory Bowel Diseases

Background The National Institutes of Health recommend a readability grade level of less than 7th grade for patient directed information. In this study, we use validated readability metrics to analyze patient information from prominent websites pertaining to ulcerative colitis and Crohn's disease. Methods The terms “Crohn's Disease,” “Ulcerative Colitis,” and “Inflammatory Bowel Disease” were queried on Google and Bing. Websites containing patient education material were saved as a text file and then modified through expungement of medical terminology that was described within the text. Modified text was then divided into subsections that were analyzed using six validated readability scales. Results None of the websites analyzed in this study achieved an estimated reading grade level below the recommended 7th grade. The median readability grade level (after modification) was 11.5 grade levels for both Crohn's disease and ulcerative colitis. The treatment subsection required the highest level of education with a median readability grade of 12th grade (range of 6.9 to 17). Conclusion Readability of online patient education material from the analyzed popular websites far exceeds the recommended level of being less than 7th grade. Patient education resources should be revised to achieve wider health literacy.
Approximate Dynamic Programming Coordinated Control in Multi-infeed HVDC Power System

This paper is concerned with large scale, interconnected, AC/DC transmission network of a power system. As the system grid becomes larger and power demand becomes higher, low frequency oscillation has become the primary concern of power system stability. High voltage direct current (HVDC) modulation control is a traditional means of damping the low frequency swing. However, for multi-infeed system, the interactions and correlations among multiple HVDC links have made the stabilizing controller design more challenging. The current approach to controller design, which only takes into consideration of a single transmission link, is not sufficient to cope with the complex network topology, and the stringent stabilization requirement of a system operating close to its limit. In this paper, a coordinated control framework using an approximate dynamic programming (ADP) technique is proposed based on wide-area measurement system (WAMS). Since real-time system responses are available through WAMS, the parameters of different controllers can be adjusted online to optimize one common objective function that reflects the system stability as a whole instead of just one single transmission link. The paper will include a design procedure on how ADP can be applied. The performance of this coordinated control approach using the proposed ADP is validated in a real system, namely the China Southern Grid
Dietary intake of soluble fiber and risk of islet autoimmunity by 5 y of age: results from the TEDDY study.

BACKGROUND Deficient soluble fiber intake has been suggested to dysregulate the immune response either directly or through alterations of the microbial composition in the gut. OBJECTIVE We hypothesized that a high intake of dietary soluble fiber in early childhood decreases the risk of type 1 diabetes (T1D)-associated islet autoimmunity. DESIGN We analyzed 17,620 food records collected between age 9 and 48 mo from 3358 children from the United States and Germany prospectively followed in the TEDDY (The Environmental Determinants of Diabetes in the Young) study. HRs for the development of any/multiple islet autoantibodies (242 and 151 events, respectively) and T1D (71 events) by soluble fiber intake were calculated in Cox regression models and adjusted for potential confounders. RESULTS There were no statistically significantly protective associations observed between a high intake of soluble fiber and islet autoimmunity or T1D. For example, the adjusted HRs (95% CIs) for high intake (highest compared with lowest quintile) at age 12 mo were 0.90 (0.55, 1.45) for any islet autoantibody, 1.20 (0.69, 2.11) for multiple islet autoantibodies, and 1.24 (0.57, 2.70) for T1D. In analyzing soluble fiber intake as a time-varying covariate, there were also no short-term associations between soluble fiber intake and islet autoimmunity development, with adjusted HRs of 0.85 (0.51, 1.42) for high intake and development of any islet autoantibody, for example. CONCLUSION These results indicate that the intake level of dietary soluble fiber is not associated with islet autoimmunity or T1D in early life.
Towards context-aware search with right click

Many queries are submitted to search engines by right-clicking the marked text (i.e., the query) in Web browsers. Because the document being read by the searcher often provides sufficient contextual information for the query, search engine could provide much more relevant search results if the query is augmented by the contextual information captured from the source document. How to extract the right contextual information from the source document is the main focus of this study. To this end, we evaluate 7 text component extraction schemes, and 5 feature extraction schemes. The former determines from which text component (e.g., title, meta-data, or paragraphs containing the selected query) to extract contextual information; the latter determines which words or phrases to extract. In total 35 combinations are evaluated and our evaluation results show that noun phrases extracted from all paragraphs that contain the query word is the best option.
Independent Spatial-Frequency-Tuned Channels in Binocular Fusion and Rivalry

Monocular masking studies show that the visibility of a one-dimensional sinusoidal grating remains unchanged in the presence of masking noise filtered so as to contain spectral components that are at least two octaves away from the spatial frequency of the grating (Stromeyer and Julesz 1972). In the present study, random-dot stereograms were bandpass filtered in the two-dimensional Fourier domain, and masking noise of various spatial frequency bands was added to the filtered stereograms. Masking noise bands containing equally effective noise energy were selected such that their bands were either overlapping with the stereoscopic image spectrum or were two octaves distant. The first case resulted in binocular rivalry; however, in the second case stereoscopic fusion could be maintained in the presence of strong binocular rivalry owing to the masking noise. This finding indicates that spatial-frequency-tuned channels are not restricted to one-dimensional gratings but operate on two-dimensional patterns as well. Furthermore, these frequency channels are utilized in stereopsis and work independently from each other, since some of these channels can be in binocular rivalry while at the same time other channels yield fusion. The main binocular experiments are demonstrated.
Structure of the aflatoxin B(1) dialdehyde adduct formed from reaction with methylamine.

Amine conjugates of activated aflatoxin (AF) B(1) are formed in various systems, e.g., buffer amines and with protein lysine groups. Structures have been published in the literature, but the evidence is indirect in that (i) halogenated AFB(1) was usually used as the precursor and (ii) the assignment of the structure of the five-membered ring formed by cyclization is based on NMR chemical shifts. To better define these adducts and distinguish among several possibilities, we synthesized AFB(1) dialdehyde and reacted this with the surrogate methylamine at neutral pH, to simplify the system. The isolated product had the expected molecular ion (mass spectrometry) and showed pH-dependent UV spectra similar to those published for a lysine conjugate. Nuclear Overhauser enhanced spectroscopy (two-dimensional NMR, 800 MHz) of the sample (2H(2)O) showed proximity of the N-CH(3) protons only with a singlet at delta 4.10, assigned to the methylene of the added five-membered ring, but not to a delta 6.53 singlet assigned as the vinylic proton of that ring. All protons in the coumarin-furanone portion of the system were correlated to each other but not to those in the added five-membered ring. These experiments establish the structure as 2,3-dihydro-2-oxo-4-(1,2,3,4-tetrahydro-7-hydroxy-9-methoxy-3,4-dioxocyclopenta[c][1]benzopyran-6-yl)-1H-pyrrole-1-methane. The similarity of the reaction to that occurring in the reaction of AFB(1) dialdehyde with lysine and the agreement of the UV spectra suggest that this structure is applicable for the lysine analogue. The NMR results support the possible structure B of Sabbioni et al. [Sabbioni, G. , Skipper, P. L. , Buchi, G. , and Tannenbaum, S. R. (1987) Carcinogenesis 8, 819-824] and the proposed structure 8 of Sabbioni [Sabbioni, G. (1990) Chem.-Biol. Interact. 75, 1-15] but not alternative proposals. Kinetic and mechanistic considerations of the reaction of lysine with AFB(1) dialdehyde are presented in the previous article in this issue [Guengerich, F. P., Arneson, K. O. , Williams, K. M. , Deng, Z. , and Harris, T. M. (2002) Chem. Res. Toxicol. 15, 780-793].
Commit_LSN: A Novel and Simple Method for Reducing Locking and Latching in Transaction Processing Systems

This paper presents a novel and simple method, called CommitYLSN, for determining if a piece of data is in the commltted state in a transaction processing system. This method is a much cheaper alternative to the locking approach used by the prior art for this purpose. The method takes advantage of the concept of a log sequence number (LSN). In many systems. an LSN is recorded in each page of the data base to relate the state of the page to the log of update actions for that page. Our method uses information about the LSN of the first log record (call it Commit-LSN) of the oldest update transaction still executing in the system to infer that all the updates in pages with page_LSN less than Commit LSN have been committed. This reduces locking and latching. In addition. the method may also increase the level of concurrency that could be supported. The Commit LSN method makes it possible to use finegranulazty locking without unduly penalizing transactions which read numerous records. It also benefits update transactions by reducing the cost of fine-granularity locking when contention is not present for data on a page. We discuss in detail many applications of this method and illustrate its potential benefits for various environments. In order to apply the Commit-LSN method, extensions are also proposed for those systems in which (1) LSNs are not associated with pages (AS1400,’ SQLIDS, System R), (2) LSNs are used only partially (IMS), and/or (3) not all objects’ changes are logged (AS1400, SQL/DS. System R).
Ability Grouping of Crowd Workers via Reward Discrimination

We develop a mechanism for setting discriminated reward prices in order to group crowd workers according to their abilities. Generally, a worker has a certain level of confidence in the correctness of her answers, and asking about it is useful for estimating the probability of correctness. However, we need to overcome two main obstacles to utilize confidence for inferring correct answers. One is that a worker is not always well-calibrated. Since she is sometimes over/underconfident, her confidence does not always coincide with the probability of correctness. The other is that she does not always truthfully report her confidence. Thus, we design an indirect mechanism that enables a worker to declare her confidence by choosing a desirable reward plan from the set of plans that correspond to different confidence intervals. Our mechanism ensures that choosing a plan including true confidence maximizes the worker's expected utility. We also propose a method that composes a set of plans that can achieve requester-specified accuracy in estimating the correct answer using a small number of workers. We show our experimental results using Amazon Mechanical Turk.
Transcranial magnetic stimulation: a new tool in the fight against depression

Since its introduction to the clinical realm in 1985, transcranial magnetic stimulation (TMS) has rapidly developed into a tool for exploring central nervous system function in both health and disease. The antidepressant effects of TMS were initially observed in 1993. Since then, a solid body of evidence has accumulated suggesting antidepressant effects for both slow TMS (sTMS) and repetitive TMS (rTMS). This review is divided into four parts. First, it addresses the basic concepts governing TMS, and then, second, it discusses the technical parameters involved in administering TMS. Knowledge of these parameters is necessary for understanding how TMS is administered, and how manipulation of the technique impacts on the results obtained. Third, we review the most relevant studies on the antidepressant effects of sTMS and rTMS published to date. Finally, we discuss cortical excitability and how the understanding of this basic neurophysiological function of cortical neurons can be used for monitoring the effects of TMS. In our discussion, we conclude that the time has arrived for TMS to be offered to depressed patients as a treatment.
The Application of Classification and Regression Trees for the Triage of Women for Referral to Colposcopy and the Estimation of Risk for Cervical Intraepithelial Neoplasia: A Study Based on 1625 Cases with Incomplete Data from Molecular Tests

Objective. Nowadays numerous ancillary techniques detecting HPV DNA and mRNA compete with cytology; however no perfect test exists; in this study we evaluated classification and regression trees (CARTs) for the production of triage rules and estimate the risk for cervical intraepithelial neoplasia (CIN) in cases with ASCUS+ in cytology. Study Design. We used 1625 cases. In contrast to other approaches we used missing data to increase the data volume, obtain more accurate results, and simulate real conditions in the everyday practice of gynecologic clinics and laboratories. The proposed CART was based on the cytological result, HPV DNA typing, HPV mRNA detection based on NASBA and flow cytometry, p16 immunocytochemical expression, and finally age and parous status. Results. Algorithms useful for the triage of women were produced; gynecologists could apply these in conjunction with available examination results and conclude to an estimation of the risk for a woman to harbor CIN expressed as a probability. Conclusions. The most important test was the cytological examination; however the CART handled cases with inadequate cytological outcome and increased the diagnostic accuracy by exploiting the results of ancillary techniques even if there were inadequate missing data. The CART performance was better than any other single test involved in this study.