Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction to the Research Direction

In my opinion, the ultimate goal of NLP is to create a computer that really understands the meaning and information conveyed by a Natural Language (NL) text or speech. From a practical point of view, we would like computers to read and understand information in texts so that they could answer correctly questions about that information.2 From a scientific perspective, if a computer is able to understand a class of texts correctly, knowing how it does it might shed some interesting light on how humans do it. We need to define what is meant by “understanding the meaning and information in a text. ” We take the operationalized definition: the ability to draw inferences from the text and answer questions about it in the same way that humans would given the same input. Since humans do not always agree about the inferences and answers to questions from a given NL text, we concentrate our research here on those cases where most people do agree, cases that are quite clear cut.
A new fusion framework for multispectral face recognition in the texture space

In this work, we introduce a new fusion framework for multispectral face recognition in the textures space. Active and passive infrared imaging modalities are used and comparison with visible face recognition is performed. The proposed texture space is based on the use of LBP (Local Binary Pattern) and LTP (Local Ternary Pattern) techniques. Also, a new adaptive texture descriptor is presented. This last descriptor called LATP (Local Adaptive Ternary Pattern) is less sensitive to noise in near uniform regions and permit to overcome some of the limitations of LBP and LTP descriptors. The obtained multispectral data are fused using a multi-scale fusion scheme in order to get interesting face characteristics. The obtained results are promising and show an increase in recognition performance when texture channels are fused in a multi-scale fusion scheme.
PREDICT-2ND: a tool for generalized protein local structure prediction

MOTIVATION Predictions of protein local structure, derived from sequence alignment information alone, provide visualization tools for biologists to evaluate the importance of amino acid residue positions of interest in the absence of X-ray crystal/NMR structures or homology models. They are also useful as inputs to sequence analysis and modeling tools, such as hidden Markov models (HMMs), which can be used to search for homology in databases of known protein structure. In addition, local structure predictions can be used as a component of cost functions in genetic algorithms that predict protein tertiary structure. We have developed a program (predict-2nd) that trains multilayer neural networks and have applied it to numerous local structure alphabets, tuning network parameters such as the number of layers, the number of units in each layer and the window sizes of each layer. We have had the most success with four-layer networks, with gradually increasing window sizes at each layer. RESULTS Because the four-layer neural nets occasionally get trapped in poor local optima, our training protocol now uses many different random starts, with short training runs, followed by more training on the best performing networks from the short runs. One recent addition to the program is the option to add a guide sequence to the profile inputs, increasing the number of inputs per position by 20. We find that use of a guide sequence provides a small but consistent improvement in the predictions for several different local-structure alphabets. AVAILABILITY Local structure prediction with the methods described here is available for use online at http://www.soe. ucsc.edu/compbio/SAM_T08/T08-query.html. The source code and example networks for PREDICT-2ND are available at http://www.soe. ucsc.edu/~karplus/predict-2nd/ A required C++ library is available at http://www.soe. ucsc.edu/~karplus/ultimate/
Using Positive Psychology to Bolster Student Success at GateWay Community College

Supported by a situational analysis and review of positive psychological literature, this paper outlines an application plan to support GateWay Community College’s ‘experiential learning with a purpose' vision which focuses on infusing meaning into students’ career development and learning. This vision was articulated by Kerry Sanderson, Director of Career Services, and Jessica Brosilo, Service Learning Center Coordinator, in the form of three guiding principles for our work: 1) accessing large student populations, 2) developing students' personal meaning and understanding of purpose through career goals, and 3) cultivating a broader view of success beyond career goals. Future-mindedness and self-efficacy emerged as key pillars in an integrative system for building meaning, along with the importance of persistence which surfaced through our discussions with Sanderson and Brosilo and our review of the Maricopa County Community College District and GateWay Community College’s joint strategic direction on student support goals. Our application plan rests on these three pillars: future-mindedness, self-efficacy, and meaning – with persistence running as a key thread throughout. The plan resides on three key processes: 1) administering a foundational, future-oriented writing exercise for incoming students that also cultivates foundations for self-efficacy and goal setting; 2) administering a growth mindset, belonging and selfefficacy intervention focused on messaging and environmental for incoming students, and 3) ongoing programming for students that supports purpose and meaning as well as student persistence.
Stability, Optimality and Complexity of Network Games with Pricing and Player Dropouts

We study basic properties of a class of noncooperative games whose players are selfish, distributed users of a network and the game's broad objective is to optimize Quality of Service (QoS) provision. This class of games was previously introduced by the authors and is a generalization of well-studied network congestion games. The overall goal is to determine a minimal set of static game rules based on pricing that result in stable and near optimal QoS provision. We show the following. (i) Standard techniques for exhibiting stability or existence of Nash equilibria fail for these games—specifically, neither are the utility functions convex, nor does a generalized potential function exist. (ii) The problem of finding whether a specific game instance in this class has a Nash equilibrium is NP-complete. To offset the apparent instability of these games, we show positive results. (iii) For natural subclasses of these games, although generalized potential functions do not exist, approximate Nash equilibria do exist and are easy to compute. (iv) These games perform well in terms of price of stability and price of anarchy. I.e., all of these approximate Nash equilibria nearly optimize a communal (or social) welfare function, and there is atleast one Nash equilibrium that is optimal. Finally, we give computer experiments illustrating the basic dynamics of these games which indicate that price thresholds could speed up convergence to Nash equilibria.
An algorithm for detecting homologues of known structured RNAs in genomes

Distinct RNA structures are frequently involved in a wide-range of functions in various biological mechanisms. The three dimensional RNA structures solved by X-ray crystallography and various well-established RNA phylogenetic structures indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop region. Discovery of well-ordered RNA structures and their homologues in genome-wide searches will enhance our ability to detect the RNA structural motifs and help us to highlight their association with functional and regulatory RNA elements. We present here a novel computer algorithm, HomoStRscan, that takes a single RNA sequence with its secondary structure to search for homologous RNAs in complete genomes. This novel algorithm completely differs from other currently used search algorithms of homologous structures or structural motifs. For an arbitrary segment (or window) given in the target sequence, that has similar size to the query sequence, HomoStRscan finds the most similar structure to the input query structure and computes the maximal similarity score (MSS) between the two structures. The homologous RNA structures are then statistically inferred from the MSS distribution computed in the target genome. The method provides a flexible, robust and fine search tool for any homologous structural RNAs.
Use of microdialysis in translational pharmacological research

Kehr Jan*, Takashi Yoshitake, Bengt Dahlström, Folke Sjöberg 1 Pronexus Analytical AB, Grindstuvägen 44, 167 33 Bromma, Sweden. 2 Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden. 3 CTC Clinical Trial Consultants AB, Sveavägen 8, 752 36 Uppsala, Sweden. 4 Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, 581 85 Linköping, Sweden.
Towards Static Flow-Based Declassification for Legacy and Untrusted Programs

Simple non-interference is too restrictive for specifying and enforcing information flow policies in most programs. Exceptions to non-interference are provided using declassification policies. Several approaches for enforcing declassification have been proposed in the literature. In most of these approaches, the declassification policies are embedded in the program itself or heavily tied to the variables in the program being analyzed, thereby providing little separation between the code and the policy. Consequently, the previous approaches essentially require that the code be trusted, since to trust that the correct policy is being enforced, we need to trust the source code. In this paper, we propose a novel framework in which declassification policies are related to the source code being analyzed via its I/O channels. The framework supports many of the of declassification policies identified in the literature. Based on flow-based static analysis, it represents a first step towards a new approach that can be applied to untrusted and legacy source code to automatically verify that the analyzed program complies with the specified declassification policies. The analysis works by constructing a conservative approximation of expressions over input channel values that could be output by the program, and by determining whether all such expressions satisfy the declassification requirements stated in the policy. We introduce a representation of such expressions that resembles tree automata. We prove that if a program is considered safe according to our analysis then it satisfies a property we call Policy Controlled Release, which formalizes information-flow correctness according to our notion of declassification policy. We demonstrate, through examples, that our approach works for several interesting and useful declassification policies, including one involving declassification of the average of several confidential values.
Rapid Prototyping of Concave Microwells for the Formation of 3D Multicellular Cancer Aggregates for Drug Screening

Microwell technology has revolutionized many aspects of in vitro cellular studies from 2D traditional cultures to 3D in vivo‐like functional assays. However, existing lithography‐based approaches are often costly and time‐consuming. This study presents a rapid, low‐cost prototyping method of CO2 laser ablation of a conventional untreated culture dish to create concave microwells used for generating multicellular aggregates, which can be readily available for general laboratories. Polymethylmethacrylate (PMMA), polydimethylsiloxane (PDMS), and polystyrene (PS) microwells are investigated, and each produces distinctive microwell features. Among these three materials, PS cell culture dishes produce the optimal surface smoothness and roundness. A549 lung cancer cells are grown to form cancer aggregates of controllable size from ≈40 to ≈80 μm in PS microwells. Functional assays of spheroids are performed to study migration on 2D substrates and in 3D hydrogel conditions as a step towards recapitulating the dissemination of cancer cells. Preclinical anti‐cancer drug screening is investigated and reveals considerable differences between 2D and 3D conditions, indicating the importance of assay type as well as the utility of the present approach.
Purinergic stimulation of K+-dependent Na+/Ca2+ exchanger isoform 4 requires dual activation by PKC and CaMKII

K+-dependent Na+/Ca2+-exchanger isoform 4 (NCXK4) is one of the most broadly expressed members of the NCKX (K+-dependent Na+/Ca2+-exchanger) family. Recent data indicate that NCKX4 plays a critical role in controlling normal Ca2+ signal dynamics in olfactory and other neurons. Synaptic Ca2+ dynamics are modulated by purinergic regulation, mediated by ATP released from synaptic vesicles or from neighbouring glial cells. Previous studies have focused on modulation of Ca2+ entry pathways that initiate signalling. Here we have investigated purinergic regulation of NCKX4, a powerful extrusion pathway that assists in terminating Ca2+ signals. NCKX4 activity was stimulated by ATP through activation of the P2Y receptor signalling pathway. Stimulation required dual activation of PKC (protein kinase C) and CaMKII (Ca2+/calmodulin-dependent protein kinase II). Mutating T312, a putative PKC phosphorylation site on NCKX4, partially prevented purinergic stimulation. These data illustrate how purinergic regulation can shape the dynamics of Ca2+ signalling by activating a signal damping and termination pathway.
MODELING THE VERY SMALL SCALE CLUSTERING OF LUMINOUS RED GALAXIES

We model the small-scale clustering of luminous red galaxies (LRGs) in the Sloan Digital Sky Survey. Specifically, we use the halo occupation distribution formalism to model the projected two-point correlation function of LRGs on scales well within the sizes of their host halos (0.016 h−1 Mpc ⩽ r ⩽ 0.42 h−1 Mpc). We start by varying P(N|M), the probability distribution that a dark matter halo of mass M contains N LRGs, and assuming that the radial distribution of satellite LRGs within halos traces the Navarro–Frenk–White (NFW) dark matter density profile. We find that varying P(N|M) alone is not sufficient to match the small-scale data. We next allow the concentration of satellite LRG galaxies to differ from that of dark matter and find that this is also not sufficient. Finally, we relax the assumption of an NFW profile and allow the inner slope of the density profile to vary. We find that this model provides a good fit to the data and the resulting value of the slope is −2.17 ± 0.12. The radial density profile of satellite LRGs within halos is thus not compatible with that of the underlying dark matter, but rather is closer to an isothermal distribution.
A robot on the shoulder: Coordinated human-wearable robot control using Coloured Petri Nets and Partial Least Squares predictions

A wearable robot secured on the shoulder of a human is developed for assisting its wearer in the execution of tasks in the overhead workspace. Installing a ceiling panel is an example of such a task. During this task the robot can hold the panel or collaborate actively with the human in order to fix the panel with the appropriate equipment. This wearable robot, termed "Supernumerary Robotic Limbs", works closely with the human to streamline the operation and reduce the human workload. First, the design concept of the Robot-on-the-Shoulder system is described, and a new approach to the coordinated control between the wearable robot and the human is presented. A graphical task process representation based on Coloured Petri Nets (CPN) is used to model the concurrent and distributed nature of the human-robot system, which comprises two human hands and two robot hands. The CPN framework is then extended to a type of hybrid control system by imbedding local dynamic controllers in the Transition nodes of the CPN model. Each local dynamic controller collects sensor signals relevant to the target transition and makes a predictive control decision. This allows the robot on the shoulder to take a proactive and preemptive action as well as to confirm a successful Transition. The control parameters for these algorithms are tuned based on "teaching-by-showing" techniques using human demonstration data. Partial Least Squares is used for extracting significant sensor signals from high-dimensional sensor data in order to do real time predictions and control. A prototype robot-on-the-shoulder system is built, and the CPN hybrid control is implemented and tested for a ceiling panel installation task.
Louse- and flea-borne rickettsioses: biological and genomic analyses

In contrast to 15 or more validated and/or proposed tick-borne spotted fever group species, only three named medically important rickettsial species are associated with insects. These insect-borne rickettsiae are comprised of two highly pathogenic species, Rickettsia prowazekii (the agent of epidemic typhus) and R. typhi (the agent of murine typhus), as well as R. felis, a species with unconfirmed pathogenicity. Rickettsial association with obligate hematophagous insects such as the human body louse (R. prowazekii transmitted by Pediculus h. humanus) and several flea species (R. typhi and R. felis, as well as R. prowazekii in sylvatic form) provides rickettsiae the potential for further multiplications, longer transmission cycles and rapid spread among susceptible human populations. Both human body lice and fleas are intermittent feeders capable of multiple blood meals per generation, facilitating the efficient transmission of rickettsiae to several disparate hosts within urban/rural ecosystems. While taking into consideration the existing knowledge of rickettsial biology and genomic attributes, we have analyzed and summarized the interacting features that are unique to both the rickettsiae and their vector fleas and lice. Furthermore, factors that underlie rickettsial changing ecology, where native mammalian populations are involved in the maintenance of rickettsial cycle and transmission, are discussed.
Estimating the Rate of Return to Education using Microsimulation

This paper attempts to use microsimulation methods to compare returns to education in four European countries, Germany, Ireland, Italy and the United Kingdom. This paper broadens the type of measure used to measure the return to education to include interactions with public taxtransfer systems and to consider the effect of differential employment rates on education. Mincer style wage equations are estimated for each country in order to model the return to education of gross earnings. These estimates are then incorporated into a microsimulation model to estimate social, private and fiscal returns to education in the countries. Both point estimates and a distribution of the rates of return are described.
Unexpectedly, Cluster Headache does not appear to involve a cardiac autonomic problem, as reflected by continuous wavelet transform

Cluster headache is a severe form of the primary headache syndromes, yet the basic pathology is unknown. We examined cardiac autonomic function in 14 subjects with Cluster Headache (CH) during headache period and 11 subjects in "quiescent" period (QP) versus a control group (C ,n=9). Subjects rested supine for 30 min before performing: Isometric Handgrip (HG) and Active Change in Posture (CP). Time frequency analysis of respiration, heart rate (HR) and continuous blood pressure (BP) was performed using a modified Continuous Wavelet Transform (CWT). There were no differences in HR or spectral content ofHR at any time. LF fluctuations in BP in response to CP were significantly greater in C compared with CH or QP. During HG, QP had significantly greater increases in BP than CH or C, despite similar LF of BP. We conclude that cardiac autonomic control is normal in CH, but less LF fluctuations in BP are required to increase BP.
Different Neural Circuits Subserve Reading before and after Therapy for Acquired Dyslexia

Rehabilitative measures for stroke are not generally based on basic neurobiological principles, despite evidence from animal models that certain anatomical and pharmacological changes correlate with recovery. In this report, we use functional magnetic resonance imaging (fMRI) to study in vivo human brain reorganization in a right handed patient with an acquired reading disorder from stroke. With phonological dyslexia, her whole-word (lexical) reading approach included inability to read nonwords and poor reading of function words. Following therapy, she was able to read nonwords and function words, and preferred a decompositional (sub-lexical) strategy in general. fMRI was performed during a reading task before and after treatment. Prior to therapy, her main focus of brain activation was in the left angular gyrus (area 39). After therapy, it was instead in the left lingual gyrus (area 18). This result suggests first that it is possible to alter brain physiology with therapy for acquired language disorders, and second, that two reading strategies commonly used in normal reading use distinct neural circuits, possibly reconciling several conflicting neuroimaging studies of reading.
Enhancing counseling services for Black college women attending HBCUs

ABSTRACT Black women’s college experiences are often compounded with psychological stressors such as race- and gender-related oppression, which may influence psychosocial adjustment. Generally, college students experiencing difficulties with psychosocial adjustment will often access college counseling services to manage their experiences. However, for many Black college women, issues related to mistrust of mental health practitioners, cultural barriers, economic factors, and reliance on friends and family result in their underutilization of professional services. Using an experimental design composed of an intervention group and a non-treatment control group with pretest and posttest measures, this study examined the effectiveness of a psychoeducational group intervention involving 20 undergraduate Black college women. Results revealed that after the 10-week group program, participants decreased their external locus of control significantly compared with members of the control group. The difference remained statistically significant after control variables were taken into account. However, the data failed to support the hypotheses that the intervention would have a statistically significant effect on perceived stress and increasing active coping. Although this study was conducted with a small sample of Black college women who attend Historically Black Colleges and Universities (HBCUs), the findings offer preliminary data on the effectiveness of culture-relevant-based group interventions with Black women aimed at enhancing psychosocial competence and reducing stress.