Miracle-dz/UniFAR-FTUs huggingface dataset:
TREC-9 Cross Language, Web and Question-Answering Track Experiments using PIRCS

Abstract : In TREC-9, we participated in the English-Chinese Cross Language, 10GB Web data ad-hoc retrieval, as well as the Question-Answering tracks, all using automatic procedures. All these tracks were new for us. For Cross Language track, we made use of two techniques of query translation: MT software and bilingual wordlist lookup with disambiguation. The retrieval lists from them were then combined as our submitted results. One submitted run used wordlist translation only. All cross language runs make use of the previous TREC Chinese collection for enrichment. One MT run also employs pre-translation query expansion using TREC English collections. We also submitted a monolingual run without collection enrichment. Evaluation shows that English-Chinese cross-lingual retrieval using only wordlist query translation can achieve about 70-75% of monolingual average precision, and combination with MT query translation further brings this effectiveness to 80-85% of monolingual. Results are well above median.
Desmoglein 3, its pathogenecity and a possibility for therapeutic target in pemphigus vulgaris

Introduction: Desmoglein 3 (Dsg3) is one of desmosomal cadherins and functions in epidermal keratinocyte adhesion. IgG anti-Dsg3 autoantibodies are detected in pemphigus vulgaris, an autoimmune bullous disease showing blisters and erosions on the skin and oral mucosa. Other types of pemphigus also show anti-Dsg3 antibodies. Genetic disease of Dsg3 has not been reported. Areas covered: Many in vitro and in vivo studies have indicated pathogenic role of anti-Dsg3 antibodies. Blisters in pemphigus vulgaris are thought to be developed by loss of keratinocyte adhesions by binding of anti-Dsg3 antibodies to Dsg3 through steric hindrance, internalization of Dsg3, changes in molecular integrity or signal transduction. There are pathogenic and nonpathogenic anti-Dsg3 antibodies reactive with different epitopes. Recent studies of pemphigus vulgaris include existence of non-Dsg3 autoantibodies, B cells and T cells reactive with Dsg3, involvement of TNF-α and IL-1 and activation of intracellular signaling. Expert opinion: Although systemic corticosteroids and immunosuppressive agents are mainstays for treatment of pemphigus, intravenous immunoglobulin, plasmapheresis, immunoadsorption, rituximab and TNF-α inhibitors are emerging. Anti-Dsg3 antibody-targeting therapies are reported in mouse model, but they are not yet available clinically. Clarification of pathogenic role of anti-Dsg3 antibodies in pemphigus should provide us with safer and more effective therapies.
Functional connectivity mapping of regions associated with self‐ and other‐processing

Neuroscience literature increasingly suggests a conceptual self composed of interacting neural regions, rather than independent local activations, yet such claims have yet to be investigated. We, thus, combined task‐dependent meta‐analytic connectivity modeling (MACM) with task‐independent resting‐state (RS) connectivity analysis to delineate the neural network of the self, across both states. Given psychological evidence implicating the self's interdependence on social information, we also delineated the neural network underlying conceptual other‐processing. To elucidate the relation between the self‐/other‐networks and their function, we mined the MACM metadata to generate a cognitive–behavioral profile for an empirically identified region specific to conceptual self, the pregenual anterior cingulate (pACC), and conceptual other, posterior cingulate/precuneus (PCC/PC). Mining of 7,200 published, task‐dependent, neuroimaging studies, using healthy human subjects, yielded 193 studies activating the self‐related seed and were conjoined with RS connectivity analysis to delineate a differentiated self‐network composed of the pACC (seed) and anterior insula, relative to other functional connectivity. Additionally, 106 studies activating the other‐related seed were conjoined with RS connectivity analysis to delineate a differentiated other‐network of PCC/PC (seed) and angular gyrus/temporoparietal junction, relative to self‐functional connectivity. The self‐network seed related to emotional conflict resolution and motivational processing, whereas the other‐network seed related to socially oriented processing and contextual information integration. Notably, our findings revealed shared RS connectivity between ensuing self‐/other‐networks within the ventromedial prefrontal cortex and medial orbitofrontal cortex, suggesting self‐updating via integration of self‐relevant social information. We, therefore, present initial neurobiological evidence corroborating the increasing claims of an intricate self‐network, the architecture of which may promote social value processing. Hum Brain Mapp 36:1304–1324, 2015. © 2014 Wiley Periodicals, Inc.
Glimmers: Resolving the Privacy/Trust Quagmire

Users today enjoy access to a wealth of services that rely on user-contributed data, such as recommendation services, prediction services, and services that help classify and interpret data. The quality of such services inescapably relies on trustworthy contributions from users. However, validating the trustworthiness of contributions may rely on privacy-sensitive contextual data about the user, such as a user's location or usage habits, creating a conflict between privacy and trust: users benefit from a higher-quality service that identifies and removes illegitimate user contributions, but, at the same time, they may be reluctant to let the service access their private information to achieve this high quality. We argue that this conflict can be resolved with a pragmatic Glimmer of Trust, which allows services to validate user contributions in a trustworthy way without forfeiting user privacy. We describe how trustworthy hardware such as Intel's SGX can be used on the client-side---in contrast to much recent work exploring SGX in cloud services---to realize the Glimmer architecture, and demonstrate how this realization is able to resolve the tension between privacy and trust in a variety of cases.
Human Long Noncoding RNA Regulation of Stem Cell Potency and Differentiation

Because of their capability of differentiation into lineage-specific cells, stem cells are an attractive therapeutic modality in regenerative medicine. To develop an effective stem cell-based therapeutic strategy with predictable results, deeper understanding of the underlying molecular mechanisms of stem cell differentiation and/or pluripotency maintenance is required. Thus, reviewing the key factors involved in the transcriptional and epigenetic regulation of stem cell differentiation and maintenance is important. Accumulating data indicate that long noncoding RNAs (lncRNAs) mediate numerous biological processes, including stem cell differentiation and maintenance. Here, we review recent findings on the human lncRNA regulation of stem cell potency and differentiation. Although the clinical implication of these lncRNAs is only beginning to be elucidated, it is anticipated that lncRNAs will become important therapeutic targets in the near future.
Focusing Forward Genetics: A Tripartite ENU Screen for Neurodevelopmental Mutations in the Mouse

The control of growth, patterning, and differentiation of the mammalian forebrain has a large genetic component, and many human disease loci associated with cortical malformations have been identified. To further understand the genes involved in controlling neural development, we have performed a forward genetic screen in the mouse (Mus musculus) using ENU mutagenesis. We report the results from our ENU screen in which we biased our ascertainment toward mutations affecting neurodevelopment. Our screen had three components: a careful morphological and histological examination of forebrain structure, the inclusion of a retinoic acid response element-lacZ reporter transgene to highlight patterning of the brain, and the use of a genetically sensitizing locus, Lis1/Pafah1b1, to predispose animals to neurodevelopmental defects. We recovered and mapped eight monogenic mutations, seven of which affect neurodevelopment. We have evidence for a causal gene in four of the eight mutations. We describe in detail two of these: a mutation in the planar cell polarity gene scribbled homolog (Drosophila) (Scrib) and a mutation in caspase-3 (Casp3). We find that refining ENU mutagenesis in these ways is an efficient experimental approach and that investigation of the developing mammalian nervous system using forward genetic experiments is highly productive.
Atrioventricular block and wiry hair in Teebi hypertelorism syndrome

We report on a 4½‐year‐old girl with clinical features of Teebi hypertelorism syndrome (THS), including a prominent forehead with a widow's peak, heavy and broad eyebrows, hypertelorism, long palpebral fissures, ptosis, a thin upper lip, a grooved chin, and a left preauricular cyst. She required a pacemaker for third degree atrioventricular (AV) block, a finding that has not been previously reported in 36 other patients with THS and for which we were unable to identify other causes. We have reviewed the previous reports of THS and note a characteristic facial appearance with hypertelorism, heavy, broad, and arched eyebrows, a thin upper lip with a long and deep philtrum, and a prominent forehead. Structural cardiac defects were present in five patients, implying that cardiac investigations are warranted in patients with a cardiac murmur and a clinical diagnosis of THS. © 2006 Wiley‐Liss, Inc.
Probabilistic Relational Planning with First Order Decision Diagrams

Dynamic programming algorithms have been successfully applied to propositional stochastic planning problems by using compact representations, in particular algebraic decision diagrams, to capture domain dynamics and value functions. Work on symbolic dynamic programming lifted these ideas to first order logic using several representation schemes. Recent work introduced a first order variant of decision diagrams (FODD) and developed a value iteration algorithm for this representation. This paper develops several improvements to the FODD algorithm that make the approach practical. These include, new reduction operators that decrease the size of the representation, several speedup techniques, and techniques for value approximation. Incorporating these, the paper presents a planning system, FODD-PLANNER, for solving relational stochastic planning problems. The system is evaluated on several domains, including problems from the recent international planning competition, and shows competitive performance with top ranking systems. This is the first demonstration of feasibility of this approach and it shows that abstraction through compact representation is a promising approach to stochastic planning.
Direct activation of Shroom3 transcription by Pitx proteins drives epithelial morphogenesis in the developing gut

Individual cell shape changes are essential for epithelial morphogenesis. A transcriptional network for epithelial cell shape change is emerging in Drosophila, but this area remains largely unexplored in vertebrates. The distinction is important as so far, key downstream effectors of cell shape change in Drosophila appear not to be conserved. Rather, Shroom3 has emerged as a central effector of epithelial morphogenesis in vertebrates, driving both actin- and microtubule-based cell shape changes. To date, the morphogenetic role of Shroom3 has been explored only in the neural epithelium, so the broad expression of this gene raises two important questions: what are the requirements for Shroom3 in non-neural tissues and what factors control Shroom3 transcription? Here, we show in Xenopus that Shroom3 is essential for cell shape changes and morphogenesis in the developing vertebrate gut and that Shroom3 transcription in the gut requires the Pitx1 transcription factor. Moreover, we show that Pitx proteins directly activate Shroom3 transcription, and we identify Pitx-responsive regulatory elements in the genomic DNA upstream of Shroom3. Finally, we show that ectopic expression of Pitx proteins is sufficient to induce Shroom3-dependent cytoskeletal reorganization and epithelial cell shape change. These data demonstrate new breadth to the requirements for Shroom3 in morphogenesis, and they also provide a cell-biological basis for the role of Pitx transcription factors in morphogenesis. More generally, these results provide a foundation for deciphering the transcriptional network that underlies epithelial cell shape change in developing vertebrates.
Relationship between drainage catheter location and postoperative recurrence of chronic subdural hematoma after burr-hole irrigation and closed-system drainage.

OBJECT This study was conducted to determine the best position for the subdural drainage catheter to achieve a low recurrence rate after burr-hole irrigation and closed-system drainage of chronic subdural hematoma (CSDH). METHODS The authors studied 63 patients with CSDH in whom the drainage catheter tip was randomly placed and precisely determined on postoperative computerized tomography (CT) scans and 104 patients with CSDH in whom CT scans were obtained 7 days postsurgery. The location of the subdural drainage catheter, the maximum postoperative width of the subdural space, and the percentage of the ipsilateral subdural space occupied by air postoperatively were determined and compared with the postoperative recurrence and reoperation rates. Patients with parietal or occipital drainage had a higher rate of CSDH recurrence and much more subdural air than those with frontal drainage. In addition, patients with residual subdural air demonstrated on CT scans obtained 7 days postsurgery also had a higher recurrence rate than those without subdural air collections. Furthermore, patients with a subdural space wider than 10 mm on CT scans obtained 7 days postsurgery had a higher recurrence rate than those with a space measuring 10 mm or less. CONCLUSIONS The incidence of postoperative fluid reaccumulation seems to be reduced by placing the tip of the drainage catheter in the frontal convexity and by removing subdural air during or after surgery.
Immunopathology of herpetic stromal keratitis: discordance in CD4+ T cell function between euthymic host and reconstituted SCID recipients.

Infection of the mouse cornea with herpes simplex virus (HSV) results in an immunopathologic disease of the eye termed herpetic stromal keratitis (HSK), in which the principal orchestrator is the CD4+ T cell. The mouse genotype largely determines susceptibility or resistance to HSK. BALB/c mice (H2dIgh-1a) are susceptible, while its congenic C.B-17 strain (H2dIgh-1b), which differs only in the Ig heavy chain locus, is resistant to HSK. As the magnitude and duration of viral replication as well as anti-HSV immune responses were similar in both strains, it was determined whether resistance was due to failure of CD4+ T cells to organize the immunopathologic reaction. Adoptive transfer of HSV-primed or naive CD4+ T cells from resistant C.B-17 strain into HSV-infected SCID mice resulted in HSK lesions indistinguishable from those caused by similar transfers of BALB/c CD4+ T cells. Similar results were obtained with transfers of whole T cell populations as well as with unfractionated splenocytes from the resistant mice. These results show that while intact C.B-17 mice exhibit resistance to HSK, they possess potentially pathogenic CD4+ T cells in their repertoire. The data suggest that the HSV-infected SCID mouse provides a proinflammatory microenvironment that overrides regulatory controls and/or cause activation of quiescent cells into aggressive effector T cells that orchestrate HSK.
Theoretical Principles of Multiscale Spatiotemporal Control of Neuronal Networks: A Complex Systems Perspective

Success in the fine control of the nervous system depends on a deeper understanding of how neural circuits control behavior. There is, however, a wide gap between the components of neural circuits and behavior. We advance the idea that a suitable approach for narrowing this gap has to be based on a multiscale information-theoretic description of the system. We evaluate the possibility that brain-wide complex neural computations can be dissected into a hierarchy of computational motifs that rely on smaller circuit modules interacting at multiple scales. In doing so, we draw attention to the importance of formalizing the goals of stimulation in terms of neural computations so that the possible implementations are matched in scale to the underlying circuit modules.
IL-4Rα-Dependent Alternative Activation of Macrophages Is Not Decisive for Mycobacterium tuberculosis Pathology and Bacterial Burden in Mice

Classical activation of macrophages (caMph or M1) is crucial for host protection against Mycobacterium tuberculosis (Mtb) infection. Evidence suggests that IL-4/IL-13 alternatively activated macrophages (aaMph or M2) are exploited by Mtb to divert microbicidal functions of caMph. To define the functions of M2 macrophages during tuberculosis (TB), we infected mice deficient for IL-4 receptor α on macrophages (LysMcreIL-4Rα-/lox) with Mtb. We show that absence of IL-4Rα on macrophages does not play a major role during infection with Mtb H37Rv, or the clinical Beijing strain HN878. This was demonstrated by similar mortality, bacterial burden, histopathology and T cell proliferation between infected wild-type (WT) and LysMcreIL-4Rα-/lox mice. Interestingly, we observed no differences in the lung expression of inducible nitric oxide synthase (iNOS) and Arginase 1 (Arg1), well-established markers for M1/M2 macrophages among the Mtb-infected groups. Kinetic expression studies of IL-4/IL-13 activated bone marrow-derived macrophages (BMDM) infected with HN878, followed by gene set enrichment analysis, revealed that the MyD88 and IL-6, IL-10, G-CSF pathways are significantly enriched, but not the IL-4Rα driven pathway. Together, these results suggest that IL-4Rα-macrophages do not play a central role in TB disease progression.
EmotionSense: a mobile phones based adaptive platform for experimental social psychology research

Today's mobile phones represent a rich and powerful computing platform, given their sensing, processing and communication capabilities. Phones are also part of the everyday life of billions of people, and therefore represent an exceptionally suitable tool for conducting social and psychological experiments in an unobtrusive way. de the ability of sensing individual emotions as well as activities, verbal and proximity interactions among members of social groups. Moreover, the system is programmable by means of a declarative language that can be used to express adaptive rules to improve power saving. We evaluate a system prototype on Nokia Symbian phones by means of several small-scale experiments aimed at testing performance in terms of accuracy and power consumption. Finally, we present the results of real deployment where we study participants emotions and interactions. We cross-validate our measurements with the results obtained through questionnaires filled by the users, and the results presented in social psychological studies using traditional methods. In particular, we show how speakers and participants' emotions can be automatically detected by means of classifiers running locally on off-the-shelf mobile phones, and how speaking and interactions can be correlated with activity and location measures.
Development of urine glucose level monitor for home healthcare using near infrared spectroscopy

We have been developing a urine glucose level monitoring technique using near infrared spectroscopy in conjunction with the chemometric method aiming for the use of home health care. In this study, validity of the calibration models were assessed using urine samples from nine healthy male subjects. For the individual measurement, reasonable accuracy was obtained in predicting urine glucose level for each subject (mean value of standard error of prediction; 25.8 mg/dl, S.D.; 10.8 mg/dl), however, the accuracy decreased (around 60 mg/dl) when the calibration models were generated using data from multiple subjects. One of the causative factors seemed to be urine urea concentration level which may vary within very wide range (0-2000 mg/dl) under physiological condition, and therefore, it was suggested that any idea, e.g., classification of data by urea level, would be required for improving the accuracy.
Results of Percutaneous Longitudinal Tenotomy for Achilles Tendinopathy in Middle- and Long-Distance Runners

From August 1989 to January 1995 we performed multiple percutaneous longitudinal tenotomies under local anesthetic on 52 middle- and long-distance run ners with unilateral Achilles tendinitis or peritendinitis that had failed conservative treatment. Forty-eight pa tients were reviewed at an average of 22.1 months (SD, 6.5) after surgery. Results were rated as excellent in 25 patients, good in 12, fair in 7, and poor in 4. Four patients developed subcutaneous hematomas. One patient developed a superficial infection at one of the incision sites, which was managed by oral antibiotics with full recovery. Three patients complained of over- sensitivity to the incisions; this was resolved by rubbing hand cream over the incisions several times a day. One patient developed hypertrophic painful scars on three of the five incisions, but corticosteroid injections yielded good functional and cosmetic results. Isometric strength and endurance of the gastrocsoleus complex was measured just before the procedure, and at 6 weeks and 6 months later. Both were within 10% of the normal contralateral limb by the 6th postoperative month. Percutaneous longitudinal tenotomy is simple, can be performed on an outpatient basis, requires minimal follow-up care, and, in our experience, has produced no significant complications. We use this procedure as the operative treatment of choice for cases of chronic tendinitis that have failed conservative treatment.
Asymptotic analysis of noise sensitivity in a neuronal burster

A combination of asymptotic approaches provides a new analysis of the effect of small noise on the bursting cycle of a neuronal burster of elliptic type (type III). The analysis is applied to a stochastic model of an excitable spine, with an activity-dependent stem conductance, that exhibits conditional burst dynamics. First, we give an asymptotic approximation to the probability density for the state of the system. This density is used to compute several quantities which describe the influence of the noise on the transition from the silent to the active phase. Second, we also use a multiscale method to provide a reduced system for analysing the effect of noise on the transition out of the active phase. The combination of these two approaches results in a new framework for a quantitative description of how noise shortens the burst cycle, which measures the significant influence of small noise. For the stochastic spine model, this study suggests that small amplitude noise can significantly influence the activity-dependent morphological plasticity of dendritic spines. The techniques used in this paper combine probabilistic and asymptotic methods, and have been generalized for other noisy nonlinear systems.