Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between Corneal Sensation, Blinking, and Tear Film Quality

Purpose To examine the possible role of corneal sensitivity and tear film quality in triggering a blink by investigating the relationship between blink rate, central corneal sensitivity threshold (CST), ocular surface temperature (OST), tear meniscus height (TMH), tear film quality (noninvasive tear break-up time [NIBUT]), and tear film lipid pattern under normal conditions. Methods Forty-two volunteers (average age, 27.76 ± 5.36 years; 11 males) with good ocular health (Ocular Surface Disease Index, <15.0) were recruited for this cross-sectional cohort study. Blink rate, CST (noncontact corneal air gas aesthesiometry, NCCA), minimum and maximum OST in the central and inferior cornea between blinks (thermal infrared camera), TMH, NIBUT, and lipid pattern of the tear film (Keeler Tearscope Plus) were recorded on the right eye only. Results Median blink rate was 11 blinks/min (interquartile range [IR], 6.95 to 17.05), CST was 0.35 mbars (IR, 0.30 to 0.40), minimum OST in the central cornea was 35.15°C (IR, 34.58 to 35.50), and NIBUT was 34.55 s (IR, 12.45 to 53.80). Moderate but statistically significant correlations were observed between CST and NIBUT (r = 0.535, p < 0.001), CST and blink rate (r = −0.398, p < 0.001), lipid pattern and OST (r = 0.556, p < 0.001), and between CST and OST (r = 0.371, p = 0.008). The correlations between blink rate and NIBUT (r = −0.696, p < 0.001) and between OST and NIBUT (r = 0.639, p < 0.001; Spearman test) achieved higher significance; this was highlighted by the linear regression model where NIBUT and minimum central and inferior OST were identified as significant predictor variables. Conclusions There is strong evidence for significant interactions between corneal sensitivity, NIBUT, OST, and blink frequency, emphasizing that ocular surface conditions represent a possible important trigger for the initiation of a blink. However, the mechanisms involved in the initiation of a blink are complex, with local ocular sensory input as only one trigger, along with other external influences and internal factors under cortical control.
An Infinite Factor Model Hierarchy Via a Noisy-Or Mechanism

The Indian Buffet Process is a Bayesian nonparametric approach that models objects as arising from an infinite number of latent factors. Here we extend the latent factor model framework to two or more unbounded layers of latent factors. From a generative perspective, each layer defines a conditional factorial prior distribution over the binary latent variables of the layer below via a noisy-or mechanism. We explore the properties of the model with two empirical studies, one digit recognition task and one music tag data experiment.
Essential role of MALT1 protease activity in activated B cell-like diffuse large B-cell lymphoma

A key element for the development of suitable anti-cancer drugs is the identification of cancer-specific enzymatic activities that can be therapeutically targeted. Mucosa-associated lymphoid tissue transformation protein 1 (MALT1) is a proto-oncogene that contributes to tumorigenesis in diffuse large B-cell lymphoma (DLBCL) of the activated B-cell (ABC) subtype, the least curable subtype of DLBCL. Recent data suggest that MALT1 has proteolytic activity, but it is unknown whether this activity is relevant for tumor growth. Here we report that MALT1 is constitutively active in DLBCL lines of the ABC but not the GCB subtype. Inhibition of the MALT1 proteolytic activity led to reduced expression of growth factors and apoptosis inhibitors, and specifically affected the growth and survival of ABC DLBCL lines. These results demonstrate a key role for the proteolytic activity of MALT1 in DLBCL of the ABC subtype, and provide a rationale for the development of pharmacological inhibitors of MALT1 in DLBCL therapy.
Document Model and Prototyping Methods for Web Engineering

This paper proposes models for managing documents in a web engineering context. First, it proposes a document model to better manage multilingual composite documents. The approach, inspired by the FRBR report, is to group all versions, translations, formats, etc. of a document in a unique document tree, putting document data and metadata at the same level. Then it proposes a model for prototyping applications, using a combination of class-based inheritance and prototype programming principles. This model applies to document models, documents views and actions. Finally, it proposes a metadata management model, laying foundations for easier integration and management of information in web applications. The proposed models are implemented in the framework Sydonie and several applications are built with the model and framework.
Characterization of Ca2+ signals induced in hippocampal CA1 neurones by the synaptic activation of NMDA receptors.

1. A combination of confocal microscopy, whole‐cell patch‐clamp recording, intracellular dialysis and pharmacological techniques have been employed to study Ca2+ signalling in CA1 pyramidal neurones, within rat hippocampal slices. 2. In the soma of CA1 neurones, depolarizing steps applied through the patch‐pipette resulted in transient increases in the fluorescence emitted by the Ca2+ indicator fluo‐3. The intensity of the fluorescence transients was proportional to the magnitude of the Ca2+ currents recorded through the pipette. Both the somatic fluorescence transients and the voltage‐activated Ca2+ currents ran down in parallel over a period of between approximately 15‐45 min. The fluorescence transients were considered, therefore, to be caused by increases in cytosolic free Ca2+. 3. Under current‐clamp conditions, high‐frequency (tetanic) stimulation (100 Hz, 1 s) of the Schaffer collateral‐commissural pathway led to compound excitatory postsynaptic potentials (EPSPs) and somatic Ca2+ transients. The somatic Ca2+ transients were sensitive to the N‐methyl‐D‐aspartate (NMDA) receptor antagonist D‐2‐amino‐5‐phosphonopentanoate (AP5; 100 microM). These transients, but not the EPSPs, disappeared with a time course similar to that of the run‐down of voltage‐gated Ca2+ currents. Tetanus‐induced somatic Ca2+ transients could not be elicited under voltage‐clamp conditions. 4. Fluorescence images were obtained from the dendrites of CA1 pyramidal neurones starting at least 30 min after obtaining whole‐cell access to the neurone. Measurements were obtained only after voltage‐gated Ca2+ channel activity had run down completely. 5. Tetanic stimulation of the Schaffer collateral‐commissural pathway resulted in compound EPSPs and excitatory postsynaptic currents (EPSCs), under current‐ and voltage‐clamp, respectively. In both cases, these were invariably associated with dendritic Ca2+ transients. In cells voltage‐clamped at ‐35 mV, the fluorescent signal increased on average 2‐fold during the tetanus and decayed to baseline values with a half‐time (t1/2) of approximately 5 s. 6. The alpha‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionate (AMPA) receptor antagonist, 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (CNQX; 10 microM) partially reduced the tetanus‐induced EPSC without affecting the Ca2+ transients. In contrast, AP5, which also depressed the EPSC, substantially reduced or eliminated the Ca2+ transients. 7. In normal (i.e. 1 mM Mg(2+)‐containing) medium, NMDA receptor‐mediated synaptic currents displayed the typical region of negative slope conductance in the peak I‐V relationship (between ‐90 and ‐35 mV). The dendritic tetanus‐induced Ca2+ transients also displayed a similar anomalous voltage dependence, decreasing in size from ‐35 to ‐90 mV. (ABSTRACT TRUNCATED AT 400 WORDS)
Up‐regulation of SOX9 in human sex‐determining region on the Y chromosome (SRY)‐negative XX males

Background In mammals, gonadal sex is normally determined by the presence or absence of the Y chromosome gene SRY. After expression of SRY in the sexually indifferent gonad, a number of genes encoding transcription factors and growth factors implicated in testis differentiation start to show male‐specific expression. However, in XX males, these genes must be up‐regulated in the absence of SRY, but the aetiology of SRY‐negative XX maleness remains unclear.
The triple helical structure and stability of collagen model peptide with 4(s)‐hydroxyprolyl‐pro‐gly units

Extensive studies on the structure of collagen have revealed that the hydroxylation of Pro residues in a variety of model peptides with the typical (X‐Y‐Gly)nrepeats (X and Y: Pro and its analogues) represents one of the major factors influencing the stability of triple helices. While(2S,4R)‐hydroxyproline (Hyp) at the position Y stabilizes the triple helix, (2S,4S)‐hydroxyproline (hyp) at the X‐position destabilizes the helix as demonstrated that the triple helix of (hyp‐Pro‐Gly)15 is less stable than that of (Pro‐Pro‐Gly)15 and that a shorter peptide (hyp‐Pro‐Gly)10 does not form the helix. To clarify the role of the hydroxyl group of Pro residues to play in the stabilization mechanism of the collagen triple helix, we synthesized and crystallized a model peptide (Pro‐Hyp‐Gly)4‐(hyp‐Pro‐Gly)2‐(Pro‐Hyp‐Gly)4 and analyzed its structure by X‐ray crystallography and CD spectroscopy. In the crystal, the main‐chain of this peptide forms a typical collagen like triple helix. The majority of hyp residues take down pucker with exceptionally shallow angles probably to relieve steric hindrance, but the remainders protrude the hydroxyl group toward solvent with the less favorable up pucker to fit in a triple helix. There is no indication of the existence of an intra‐molecular hydrogen bond between the hydroxyl moiety and the carbonyl oxygen of hyp supposed to destabilize the triple helix. We also compared the conformational energies of up and down packers of the pyrrolidine ring in Ac‐hyp‐NMe2 by quantum mechanical calculations. © © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 111–121, 2012.
An Instrumented Flume to Investigate the Mechanics of Rainfall-Induced Landslides in Unsaturated Granular Soils

The mechanics of rainfall-induced flowslides in pyroclastic soils have yet to be completely clarified. The complexity of phenomena (rainfall-induced failure in initially unsaturated granular deposits, post-failure transition to flow-like landslide) requires the use of a well-equipped small-scale flume. To this aim, flume experiments at the Second University of Naples were performed to analyze the fundamental aspects of such phenomena. A new experimental program is now being carried out to assess the performance of a time domain reflectometry device and optical fibers as indicators of impending failure. The paper describes the instrumented flume and the procedures adopted for monitoring the major aspects of slope behavior. Our first experimental results are very promising in this respect.
Modeling of Set/Reset Operations in NiO-Based Resistive-Switching Memory Devices

Resistive-switching memory (RRAM) devices are attracting a considerable interest in view of their back-end integration, fast programming, and high scalability. Prediction of the programming voltages and currents as a function of the operating conditions is an essential task for developing compact and numerical models able to handle a large number (106 - 109) of cells within an array. Based on recent experimental findings on the set and reset processes, we have developed physics-based analytical models for the set and reset operations in NiO-based RRAMs. Simulation results obtained by the analytical models were compared with experimental data for variable pulse conditions and were found consistent with data. The set transition is described by a threshold switching process at the broken conductive filament (CF), while the reset transition is viewed as a thermally driven dissolution and/or oxidation of the CF. Set and reset models are finally used for reliability predictions of failure times under constant-voltage stress (read disturb) and elevated-temperature bake (data retention).
CYTOCHEMISTRY OF TRACHOMA VIRUS REPLICATION IN TISSUE CULTURES *

As psittacosis virus replicates, a cytochemical sequence has been observed with acridine orange stain and ultraviolet illumination. ’ s 2 The viral deoxyribonucleic acid (DNA) initiates a reaction, in the course of which it is surrounded by a ribonucleic acid (RNA) matrix (red). Each red sphere (“red ball”) enlarges, multiplies, and maturates. In the course of maturation, each “red ball” goes through a sequence of color changes from red to orange to yellow to yellow-green. Only at the latter stage is the agent infective to animals and to fresh cells. Only at the latter stage will it absorb specific fluorescein-tagged antibody. This cytochemical sequence is dynamic and predictable. I t has been used in studies on the role of nucleic acids, in replication of psittacosis virus.3 z 4 Fluorinated pyrimidines have been incorporated into the process of viral biosynthesis with ensuing visual evidence of “fraudulent” RNA and “incomplete” DNA, neither of which were infectious. Addition of aminopterin to the nutrient fluid of newly infected cells interrupted development of psittacosis virus a t the “red ball” stage.6 Some antibiotics have induced cytochemically defined alterations in the pattern of viral maturation, thereby providing a tool for screening of drugs for psittacosis and related viruses. %S Thus, organizational stages in the chronology of virus replication have been demonstrated by means of inserting metabolic analogs at time intervals, which affected specific facets of the biosynthetic process. The sequence of participants thus demonstrable were folic acid, DNA, RNA, and protein. Interference at any point in this sequence interfered with the evolution of mature virus in the cultures. Most of the experimental procedures described above with psittacosis virus have been extended to trachoma virus, and the results support the familial interrelationship that has been demonstrated by other procedures. Materials and Methods
The Comparative Ecology of a Subarctic and Tropical Estuarine Ecosystem as Measured with Carbon and Nitrogen Isotopes

Abstract Animals representing different trophic levels were collected from two estuarine environments; the subarctic Strait of Georgia ( c. 50°N, 124°W) and the tropical coast of Kaohsiung ( c. 22°N, 121°E). The animals were analysed for their heavy isotope composition of carbon and nitrogen in order to determine the trophic structure of the two environments. The tropical environment showed a greater enrichment in the 13 C isotope which could be attributed to previously reported latitudinal differences in the source of carbon for photosynthesis. In both environments there was a further enrichment of 13 C at higher trophic levels which was believed to be the result of significant grazing on benthic organisms in both systems. The much higher variation in the data encountered in the tropical environment was attributed to the sharp contrast between offshore oligotrophic waters from the South China Sea and the Kuroshio current that mix with estuarine waters, within a short distance of the coast.
Parallelizing Bzip2: A Case Study in Multicore Software Engineering

We conducted a case study of parallelizing a real program for multicore computers using currently available libraries and tools. We selected the sequential Bzip2 compression program for the study because it's a computing-intensive, widely used, and relevant application in everyday life. Its source code is available, and its algorithm is well documented. In addition, the algorithm is non-trivial, but, with 8,000 LOC, the application is small enough to manage in a course.
3D facial clone based on depth patches

3D face clones can be used in many areas such as Human-Computer Interaction and as preprocessing in applications, such as emotion analysis. However, such clones should be structured and the model facial shape accurately while keeping the attributes of individuals. A structured mesh is a mesh with a known semantic and topological structure. We use a face model designed from a database of 3D face examples. These global models can produce structured clones but they do not often retain the specifics of the analyzed person. Indeed, methods using models are very dependent on their databases. In our technique, we use an RGB-D sensor to get the attributes of individuals and a 3D Morphable Face Model to mark facial shape. We reverse the process classically used: we first perform fitting and then data fusion. For each depth frame, we retain the suitable data parts called Patches. This selection is performed using a distance error and the direction of the normal vectors. Depending on the location, we merge either sensor data or 3D Morphable Face Model data. We compare our method with state of the art fitting processes. The qualitative and quantitative tests show that our results are more accurate than an current fitting method and our clone has both the attributes of the person and the shape of the face well modeled.
Prostaglandins in migraine: update.

PURPOSE OF REVIEW This review presents recent findings on the role of prostaglandins in migraine pathophysiology. RECENT FINDINGS Experimental studies have shown that prostaglandins are distributed in the trigeminal-vascular system and its receptors are localized in the trigeminal ganglion and the trigeminal nucleus caudalis. Prostaglandins were found in smooth muscles of cranial arteries, and functional studies in vivo showed that prostaglandins induced dilatation of cranial vessels. Human studies showed that intravenous infusion of vasodilating prostaglandins such as prostaglandin E₂ (PGE₂), prostaglandin I₂ (PGI₂) and prostaglandin D₂ (PGD₂) induced headache and dilatation of intra-cranial and extra-cranial arteries in healthy volunteers. In contrast, infusion of non-dilating prostaglandin F₂α (PGF₂α) caused no headache or any vascular responses in cranial arteries. PGE₂ and PGI₂ triggered migraine-like attacks in migraine patients without aura, accompanied by dilatation of the intra-cerebral and extra-cerebral arteries. A novel EP4 receptor antagonist could not prevent PGE₂-induced headache in healthy volunteers. SUMMARY Recent in-vitro/in-vivo data demonstrated presence and action of prostaglandins within the trigeminal pain pathways. Migraine induction after intravenous administration of PGE₂ and PGI₂ suggests a specific blockade of their receptors, EP and IP respectively, as a new potential drug target for the acute treatment of migraine.
Implicación del alumnado en la valoración de su satisfacción con las webs didácticas

Presentamos el proceso y resultado del esfuerzo por implicar al alumnado universitario en la valoracion de Web Didacticas. Hemos trabajado cooperativamente con alumnos y profesores, con el objetivo de conseguir un instrumento de evaluacion ajustado a la percepcion que ambos colectivos tienen del recurso. Nuestros resultados aportan un conjunto de items para valorar la satisfaccion del alumnado con las webs didacticas y la comprobacion de que ese recurso, desde una perspectiva didactica, resulta muy bien valorado por el alumnado. Implication of the student body in the appraisal of his satisfaction with the use of didactic websites Abstract We introduce the process and the results of an effort in order to implicate the universitary student body in the appraisal of their satisfaction about the use of the didactic webs. We have worked hand to hand with students and professors, with the aim to obtain an instrument of evaluation adjusted to the perception that both groups have of the resource. Our results provide a set of items to evaluate the satisfaction of the learners with the use of didactic websites and the test that this technological resource, oriented from a didactical view, is well valued by the student body.
Antiviral effect of lymphokine-activated killer cells: characterization of effector cells mediating prophylaxis

Lymphokine-activated killer (LAK) cells generated by cultivation of C57BL/6 mouse spleen cells in the presence of recombinant interleukin-2 were transferred into natural killer (NK) cell-deficient suckling mouse recipients. These mice were then challenged with either murine cytomegalovirus (MCMV) or lymphocytic choriomeningitis (LCMV) and sacrificed 3 days later. No interleukin 2 infusions were given. Mice receiving as few as 5 x 10(5) LAK cells had several 100-fold decreases in spleen MCMV titers as compared with untreated mice. This treatment had no effect on spleen LCMV titers. The LAK cell cultures contained 10 to 17% NK 1.1+, 50 to 55% Lyt-2+, and 33 to 50% immunoglobulin D+ cells. Double fluorescence labeling and in vitro cytotoxicity assays with fluorescence-activated cell sorting revealed at least two mutually exclusive killer cell populations. NK 1.1+ LAK cells resembled freshly isolated activated NK cells with regard to target cell range (YAC-1 cell killing greater than L-929, P815, and EL-4 cell killing), large granular lymphocyte (LGL) morphology, and decreased ability to lyse interferon (IFN)-treated target cells. Lyt-2+ LAK cells lysed the targets mentioned above but at lower levels and without the differences in susceptibility mentioned above. These Lyt-2+ LAK cells also had a decreased ability to lyse IFN-treated targets, in contrast to classic cytotoxic T lymphocytes, which lyse IFN-treated targets far more efficiently than untreated targets. Purified populations of LAK cells obtained by fluorescence-activated cell sorting were used in the antiviral protection model. The results showed that protection against MCMV could be mediated by NK 1.1+, NK 1.1-, Lyt-2+, Lyt-2-, and IgD- populations but not by IgD+ cells. The five protective populations all had in common the LGL phenotype and cytotoxic activity in vitro. The IgD+ population did not contain LGLs, lyse target cells in vitro, or mediate an antiviral effect in vivo. These results suggest that LAK cells may be therapeutically useful against certain virus infections (MCMV) but not others (LCMV) and that despite their heterogeneity in antigenic phenotype and cytotoxic activity, their pattern of antiviral activity in vivo resembles that of NK cells, which protect against MCMV but not LCMV.
A Singly-Exponential Time Algorithm for Computing Nonnegative Rank

Here, we give an algorithm for deciding if the nonnegative rank of a matrix $M$ of dimension $m \times n$ is at most $r$ which runs in time $(nm)^{O(r^2)}$. This is the first exact algorithm that runs in time singly-exponential in $r$. This algorithm (and earlier algorithms) are built on methods for finding a solution to a system of polynomial inequalities (if one exists). Notably, the best algorithms for this task run in time exponential in the number of variables but polynomial in all of the other parameters (the number of inequalities and the maximum degree). Hence these algorithms motivate natural algebraic questions whose solution have immediate {\em algorithmic} implications: How many variables do we need to represent the decision problem, does $M$ have nonnegative rank at most $r$? A naive formulation uses $nr + mr$ variables and yields an algorithm that is exponential in $n$ and $m$ even for constant $r$. (Arora, Ge, Kannan, Moitra, STOC 2012) recently reduced the number of variables to $2r^2 2^r$, and here we exponentially reduce the number of variables to $2r^2$ and this yields our main algorithm. In fact, the algorithm that we obtain is nearly-optimal (under the Exponential Time Hypothesis) since an algorithm that runs in time $(nm)^{o(r)}$ would yield a subexponential algorithm for 3-SAT . Our main result is based on establishing a normal form for nonnegative matrix factorization - which in turn allows us to exploit algebraic dependence among a large collection of linear transformations with variable entries. Additionally, we also demonstrate that nonnegative rank cannot be certified by even a very large submatrix of $M$, and this property also follows from the intuition gained from viewing nonnegative rank through the lens of systems of polynomial inequalities.