Miracle-dz/UniFAR-FTUs huggingface dataset:
Hup-me: inferring and reconciling a timeline of user activity from rich smartphone data

We designed a system to infer multimodal itineraries traveled by a user from a combination of smartphone sensor data (e.g., GPS, Wi-Fi, accelerometer) and knowledge of the transport network infrastructure (e.g., road and rail maps, public transportation timetables). The system uses a Transportation network that captures the set of possible paths of this network for the modes, e.g., foot, bicycle, road_vehicle, and rail. This Transportation network is constructed from OpenStreetMap data and public transportation routes published online by transportation agencies in GTFS format. The system infers itineraries from a sequence of smartphone observations in two phases. The first phase uses a dynamic Bayesian network that models the probabilistic relationship between paths in Transportation network and sensor data. The second phase attempts to match portions recognized as road_vehicle or rail with possible public transportation routes of type bus, train, metro, or tram extracted from the GTFS source. We evaluated the performance of our system with data from users traveling over the Paris area who were asked to record data for different trips via an Android application. Itineraries were annotated with modes and public transportation routes taken and we report on the results of the recognition.
Redundant or separate entities?—roles of Twist1 and Twist2 as molecular switches during gene transcription

Twist1 and Twist2 are highly conserved members of the Twist subfamily of bHLH proteins responsible for the transcriptional regulation of the developmental programs in mesenchymal cell lineages. The regulation of such processes requires that Twist1 and Twist2 function as molecular switches to activate and repress target genes by employing several direct and indirect mechanisms. Modes of action by these proteins include direct DNA binding to conserved E-box sequences and recruitment of coactivators or repressors, sequestration of E-protein modulators, and interruption of proper activator/repressor function through protein–protein interactions. Regulatory outcomes of Twist1 and Twist2 are themselves controlled by spatial-temporal expression, phosphoregulation, dimer choice and cellular localization. Although these two proteins are highly conserved and exhibit similar functions in vitro, emerging literature have demonstrated different roles in vivo. The involvement of Twist1 and Twist2 in a broad spectrum of regulatory pathways highlights the importance of understanding their roles in normal development, homeostasis and disease. Here we focus on the mechanistic models of transcriptional regulation and summarize the similarities and differences between Twist1 and Twist2 in the context of myogenesis, osteogenesis, immune system development and cancer.
Pore-scale analysis of Newtonian flow in the explicit geometry of vertebral trabecular bones using lattice Boltzmann simulation

Abstract The geometric and transport properties of trabecular bone are of particular interest for medical engineers active in orthopaedic applications and more specifically in hard tissue implantations. This article resorts to computational methods to provide some understanding of the geometric and transport properties of vertebral trabecular bone. A fuzzy distance transform algorithm was used for geometric analysis on the pore scale, and a lattice Boltzmann method (LBM) for the simulation of flow on the same scale. The transport properties of bone including the pressure drop, elongation, and shear component of dissipated energy, and the tortuosity of the bone geometry were extracted from the results of the LBM flow simulations. Whenever suitable, dimensionless numbers were used for the analysis of the data. The average pore size and distribution of the bone were found to be 746μm and between 75 and 2940μm, respectively. The permeability of the flow in the cavities of the specific bone sample was found to be 5.05×10-8 m2 for the superior—inferior direction which was by a factor of 1.5—1.7 higher than the permeability in the other two anatomical directions (anterior—posterior). These findings are consistent with experimental results found 3 years prior independently. Tortuosity values approached 1.05 for the superior—inferior direction, and 1.13 and 1.11 for the other two perpendicular directions. The low tortuosities result mainly from the large bone porosity of 0.92. The flow on the pore scale seems to be shear dominated but 30 per cent of the energy dissipation was because of elongational effects. The converging and diverging geometry of the bone explains the significant elongation and deformation of the fluid elements. The transition from creeping flow (the Darcy regime), which is of interest to vertebral augmentation and this study, to the laminar region with significant inertia effects took place at a Reynolds number of about 1—10, as usual for porous media. Finally, the authors wish to advise the readers on the significant computational requirements to be allocated to such a virtual test bench.
Ionospheric scintillation

Available observations of ionospheric scintillation are analyzed to evaluate the adequacy of existing models used for the interpretation of scintillation data. The theoretical models are reviewed and the frequency and propagation geometry dependences predicted by the models are compared with the observations. The models were used to construct scintillation occurrence distribution functions which show that scintillation phenomena significantly affect the design of transionospheric radar or communication systems operating at frequencies below 1 GHz. Diversity schemes useful for mitigation of scintillation effects are considered. Mention is made of the geophysical processes thought to be responsible for scintillation.
Marker-dependent associations among oxidative stress, growth and survival during early life in a wild mammal

Oxidative stress (OS) is hypothesized to be a key physiological mechanism mediating life-history trade-offs, but evidence from wild populations experiencing natural environmental variation is limited. We tested the hypotheses that increased early life growth rate increases OS, and that increased OS reduces first-winter survival, in wild Soay sheep (Ovis aries) lambs. We measured growth rate and first-winter survival for four consecutive cohorts, and measured two markers of oxidative damage (malondialdehyde (MDA), protein carbonyls (PC)) and two markers of antioxidant (AOX) protection (total AOX capacity (TAC), superoxide dismutase (SOD)) from blood samples. Faster lamb growth was weakly associated with increased MDA, but not associated with variation in the other three markers. Lambs with higher SOD activity were more likely to survive their first winter, as were male but not female lambs with lower PC concentrations. Survival did not vary with MDA or total TAC. Key predictions relating OS to growth and survival were therefore supported in some OS markers, but not others. This suggests that different markers capture different aspects of the complex relationships between individual oxidative state, physiology and fitness, and that overarching hypotheses relating OS to life-history variation cannot be supported or refuted by studying individual markers.
Toluene Diisocyanate Exposure: Exposure Assessment and Development of Cross-Facility Similar Exposure Groups Among Toluene Diisocyanate Production Plants

Objective: The objective of this study was to characterize workplace toluene diisocyanate (TDI) exposures using standardized industrial hygiene exposure assessment procedures for use in a prospective epidemiologic study of occupational asthma. Methods: Over 2300 representative routine full shift time-weighted average (TWA) and short-term high potential exposure tasks (HPETs) air samples in groups across three TDI plants were collected over a nearly 7-year period. Results: Data-derived similar exposure groups (SuperSEGs) were developed across the plants based on TWA sampling using cluster analysis. Individual cumulative exposure estimates were developed on the basis of the SuperSEGs. Conclusion: Workplace TWA exposures to TDI were adequately characterized quantitatively, but HPET exposures were adequately characterized only by qualitative measures. The mean TWA exposure was 0.65 parts per billion for 1594 routine samples. These TWA and HPET exposures can be used to support exposure–response analyses.
On the fusion of prosody, voice spectrum and face features for multimodal person verification

Multimodal person recognition systems normally use shortterm spectral features as voice information. In this paper prosodic information is added to a system based on face and voice spectrum features. By using two fusion techniques, support vector machines and matcher weighting, different fusion strategies based on the fusion of monomodal scores in several steps are proposed. The performance of the system is clearly improved when the prosodic information is added and the best results are achieved when prosodic scores are previously fused and the resulting scores are fused again with spectral and facial scores. Speech and face scores have been obtained upon Switchboard-I and XM2VTS databases respectively. Index Terms: speaker recognition, multimodality, fusion, prosody, voice spectrum, face
Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response

Mutators are clones whose mutation rate is about two to three orders of magnitude higher than the rate of wild-type clones and their roles in adaptive evolution of asexual populations have been controversial. Here we address this problem by using an ab initio microscopic model of living cells, which combines population genetics with a physically realistic presentation of protein stability and protein-protein interactions. The genome of model organisms encodes replication controlling genes (RCGs) and genes modeling the mismatch repair (MMR) complexes. The genotype-phenotype relationship posits that the replication rate of an organism is proportional to protein copy numbers of RCGs in their functional form and there is a production cost penalty for protein overexpression. The mutation rate depends linearly on the concentration of homodimers of MMR proteins. By simulating multiple runs of evolution of populations under various environmental stresses—stationary phase, starvation or temperature-jump—we find that adaptation most often occurs through transient fixation of a mutator phenotype, regardless of the nature of stress. By contrast, the fixation mechanism does depend on the nature of stress. In temperature jump stress, mutators take over the population due to loss of stability of MMR complexes. In contrast, in starvation and stationary phase stresses, a small number of mutators are supplied to the population via epigenetic stochastic noise in production of MMR proteins (a pleiotropic effect), and their net supply is higher due to reduced genetic drift in slowly growing populations under stressful environments. Subsequently, mutators in stationary phase or starvation hitchhike to fixation with a beneficial mutation in the RCGs, (second order selection) and finally a mutation stabilizing the MMR complex arrives, returning the population to a non-mutator phenotype. Our results provide microscopic insights into the rise and fall of mutators in adapting finite asexual populations.
Galectin‐3 expression in follicular tumours: an immunohistochemical study of its use as a marker of follicular carcinoma

Aims: Galectin‐3, a member of the beta‐galactoside binding family of lectins, has been regarded as a useful tool for discriminating malignant tumours from benign nodules of the thyroid, including the distinction between follicular carcinoma and adenoma. However, there are follicular tumours with unclear vascular or capsular invasion, which makes diagnosis more difficult. In this study, we investigated the relationship between galectin‐3 expression and the degree of vascular or capsular invasion of follicular tumours. Methods: We immunohistochemically investigated galectin‐3 expression in 260 cases of follicular tumour with various degrees of vascular or capsular invasion classified into four categories. Results: The galectin‐3 expression level significantly increased with the degree of vascular or capsular invasion (p<0.0001). However, its diagnostic value for follicular carcinoma was not high because the sensitivity and specificity were 68.7% and 57.5%, respectively. Conclusions: Our findings suggest that galectin‐3 plays a role in the transformation of follicular tumours from benign to malignant; however, when diagnosing follicular tumours, the presence of this protein should not be required for diagnosing malignant transformation in all cases. Therefore, we must conclude that galectin‐3 should only be considered an adjuvant marker for follicular carcinoma.
A Web Based Face Counter Prediction System from Only Fingerprints

Up to now a large number of approaches and algorithms about biometric recognition techniques have been developed and proposed in the literature in details. Relationships about biometrics have recently been studied in the field by author research group. This paper presents a web based intelligent face mask prediction system based on artificial neural networks to predict faces from only fingerprint images. The aim of this study is to develop an online platform to be used by users, researchers or academics around the world. The results have been shown that the system can be used for live test through internet. The proposed web based system is successful to support and encourage researchers around the world to see and exercise this new concept in biometrics. The developed system predicts an appropriate face mask covering nose, eyes, ears and mouth from fingerprint images with the help of an intelligent model.
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions

Motivation: An important problem in systems biology is reconstructing complete networks of interactions between biological objects by extrapolating from a few known interactions as examples. While there are many computational techniques proposed for this network reconstruction task, their accuracy is consistently limited by the small number of high-confidence examples, and the uneven distribution of these examples across the potential interaction space, with some objects having many known interactions and others few. Results: To address this issue, we propose two computational methods based on the concept of training set expansion. They work particularly effectively in conjunction with kernel approaches, which are a popular class of approaches for fusing together many disparate types of features. Both our methods are based on semi-supervised learning and involve augmenting the limited number of gold-standard training instances with carefully chosen and highly confident auxiliary examples. The first method, prediction propagation, propagates highly confident predictions of one local model to another as the auxiliary examples, thus learning from information-rich regions of the training network to help predict the information-poor regions. The second method, kernel initialization, takes the most similar and most dissimilar objects of each object in a global kernel as the auxiliary examples. Using several sets of experimentally verified protein–protein interactions from yeast, we show that training set expansion gives a measurable performance gain over a number of representative, state-of-the-art network reconstruction methods, and it can correctly identify some interactions that are ranked low by other methods due to the lack of training examples of the involved proteins. Contact: mark.gerstein@yale.edu Availability: The datasets and additional materials can be found at http://networks.gersteinlab. org/tse.
Learning User Preferences in Matching for Ridesharing

Sharing car journeys can be very beneficial, since it can save travel costs, as well as reducing traffic congestion and pollution. The process of matching riders and drivers automatically at short notice, is referred to as dynamic ridesharing, which has attracted a lot of attention in recent years. In this paper, amongst the wide range of challenges in dynamic ridesharing, we consider the problem of ride-matching. While existing studies mainly consider fixed assignments of participants in the matching process, our main contribution is focused on the learning of the user preferences regarding the desirability of a choice of matching; this could then form an important component of a system that can generate robust matchings that maintain high user satisfaction, thus encouraging repeat usage of the system. An SVM inspired method is exploited which is able to learn a scoring function from a set of preferences; this function measures the predicted satisfaction degree of the user regarding specific matches. To the best of our knowledge, we are the first to present a model that is able to implicitly learn individual preferences of participants. Our experimental results, which are conducted on a real ridesharing data set, show the effectiveness of our approach.
The cancer experience in the framingham heart study cohort

The almost 40‐year records of The Framingham Heart Study (FHS) cohort were reviewed to establish the cancer experience of this noninstitutionalized group of white subjects. Diagnoses were confirmed from pathology and laboratory reports and clinical notes. Age‐specific incidence rates were compared with Connecticut Surveillance, Epidemiology, and End Results (SEER) data. Among the 5209 subjects, 1201 malignancies were confirmed. Median age at diagnosis was 69 for men and 65 for women. Lung, prostate, skin, and colon accounted for more than half of men's cancers; breast, colon, and skin made up half of the women's. FHS and Connecticut SEER rates matched closely, with the same primary tumor sites appearing commonly in both groups. Thus, the FHS cohort should provide a fair database for analysis of risk factors in cancer incidence, as it has done in cardiovascular diseases.
Psychometric Comparisons of 2 Versions of the Fugl-Meyer Motor Scale and 2 Versions of the Stroke Rehabilitation Assessment of Movement

Objective. To provide empirical justification for selecting motor scales for stroke patients, the authors compared the psychometric properties (validity, responsiveness, test-retest reliability, and smallest real difference [SRD]) of the Fugl-Meyer Motor Scale (FM), the simplified FM (S-FM), the Stroke Rehabilitation Assessment of Movement instrument (STREAM), and the simplified STREAM (S-STREAM). Methods. For the validity and responsiveness study, 50 inpatients were assessed with the FM and the STREAM at admission and discharge to a rehabilitation department. The scores of the S-FM and the S-STREAM were retrieved from their corresponding scales. For the test-retest reliability study, a therapist administered both scales on a different sample of 60 chronic patients on 2 occasions. Results. Only the S-STREAM had no notable floor or ceiling effects at admission and discharge. The 4 motor scales had good concurrent validity (rho ≥ .91) and satisfactory predictive validity (rho = .72-.77). The scales showed responsiveness (effect size d ≥ 0.34; standardized response mean ≥ 0.95; P < .0001), with the S-STREAM most responsive. The test-retest agreements of the scales were excellent (intraclass correlation coefficients ≥ .96). The SRD of the 4 scales was 10% of their corresponding highest score, indicating acceptable level of measurement error. The upper extremity and the lower extremity subscales of the 4 showed similar results. Conclusions. The 4 motor scales showed acceptable levels of reliability, validity, and responsiveness in stroke patients. The S-STREAM is recommended because it is short, responsive to change, and able to discriminate patients with severe or mild stroke.
Compact Omnidirectional Antenna of Circular Polarization

A compact omnidirectional antenna of circular polarization (CP) is presented for 2.4-GHz WLAN access-point applications. The antenna consists of four bended monopoles, which are simultaneously excited through an associated feeding network. The radiated horizontal and vertical field components are derived based on an analytical model, and the 90<sup>°</sup> phase difference between them is shown to be naturally guaranteed. With a size of 0. 22λ<sub>0</sub> × 0. 22λ<sub>0</sub> × 0. 076λ<sub>0</sub>, the antenna exhibits a bandwidth (|<i>S</i><sub>11</sub>| ≤ -10 dB and AR ≤ 3 dB) of 3.56% and a left-handed CP average gain of 1.39 dB in the azimuth plane at 2.44 GHz.
Prospective Evaluation of the Toxicity Profile of Proteasome Inhibitor–Based Therapy in Renal Transplant Candidates and Recipients

Background A prospective intermediate-term evaluation of toxicities associated with bortezomib therapy for antibody-mediated rejection (AMR) and desensitization was conducted. Methods Patients were graded for bortezomib-related toxicities: hematologic and gastrointestinal toxicities by Common Terminology Criteria for Adverse Events and peripheral neuropathy by modified Functional Assessment of Cancer Therapy questionnaire and Common Terminology Criteria for Adverse Events. Results Fifty-one patients treated for AMR and 19 patients treated for desensitization received 96 bortezomib cycles (1.3 mg/m2 ×4 doses); mean (SD) follow-up was 16.3 (9.0) months. Patients treated for AMR and patients treated for desensitization were similar in age, gender, ethnicity, and baseline peripheral neuropathy. Patients treated for AMR received a mean (SD) of 4.9 (2.0) bortezomib doses in 1.3 (0.5) cycles; and patients treated for desensitization, a mean of 7.3 (1.6) doses in 1.8 (0.4) cycles. Prevalence of diabetes and anemia were higher at baseline in patients treated for AMR. In the AMR cohort, two cases of cytomegalovirus infection, two cases of BK virus infection, and one case of Epstein-Barr virus infection were observed. No cases of viral infection were observed in the desensitization cohort. Malignancies were not observed. Significant bortezomib toxicities included anemia and peripheral neuropathy, which were manageable. Anemia was more common in patients treated for AMR; and peripheral neuropathy, more common in patients treated for desensitization. Conclusions Bortezomib-related toxicities in kidney transplant candidates and recipients are low in incidence and severity and vary based on treatment population.
Preferential transport and metabolism of glucose in Bergmann glia over Purkinje cells: A multiphoton study of cerebellar slices

Knowing how different cell types handle glucose should help to decipher how energy supply is adjusted to energy demand in the brain. Previously, the uptake of glucose by cultured brain cells was studied in real‐time using fluorescent tracers and confocal microscopy. Here, we have adapted this technique to acute slices prepared from the rat cerebellum by means of multiphoton microscopy. The transport of the fluorescent glucose analogs 2NBDG and 6NBDG was several‐fold faster in the molecular layer of the cerebellar cortex than in Purkinje cell somata and granule cells. After washout of free tracer, it became apparent that most phosphorylated tracer was located in Bergmann glia, which was confirmed by counterstaining with the glial marker sulforhodamine 101. The effective recovery of fluorescence after photobleaching showed that 2NBDG‐P can diffuse horizontally across the molecular layer, presumably through gap junctions between Bergmann glial cells. Our main conclusion is that in acute cerebellar slices, the glucose transport capacity and glycolytic rate of Bergmann glia are several‐fold higher than those of Purkinje cells. Given that the cerebellum is largely fueled by glucose and Purkinje neurons are estimated to spend more energy than Bergmann glial cells, these results suggest substantial shuttling of an energy‐rich metabolite like lactate between glial cells and neurons. © 2008 Wiley‐Liss, Inc.