Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of respiratory system input impedance and bronchodilator response in healthy Finnish preschool children

In order to study the determinants of respiratory system impedance and bronchodilator response in preschool children, a sample (n=109) of healthy children (age 2·1–7·0 years) attending kindergarten was measured by using the impulse oscillometry. Their selection was based on a standardized questionnaire, negative skin prick test results and clinical examination, and sufficient cooperation. Triple measurements of respiratory resistance (Rrs) and reactance (Xrs) at 5, 10, 15 and 20 Hz, total respiratory impedance (Zrs), the resonance frequency (Fr) and the frequency dependence of resistance (dRrs/df) were performed, to determine individual mean values. Measurements were repeated after inhalation of 300 μg salbutamol (n=89) or placebo (n=19). At the baseline, Zrs and Rrs5‐20 showed negative, and Xrs5‐20, Fr and dRrs/df positive correlations with age, height and weight. However, logarithmic transformed height was the best independent variable for the regression equations of all the oscillometric variables. After inhalation of placebo, none of the oscillometric variables changed significantly. In the salbutamol group, the mean (SD) change in Rrs5 was −0·187 (0·124) kPa l–1 s–1 and –19·2 (10·2)%, corresponding to a lower reference limit of –36·9%. Both the within‐test and between‐test repeatabilities for the measurement of respiratory resistance were acceptable, for Rrs5 the coefficients of variation being 6·2 and 6·1%, respectively. As the overall success rate in our sample was high (89%), the forced oscillation technique seems to be a useful method in assessing respiratory function and bronchial lability in preschool children.
Inferring species roles in metacommunity structure from species co-occurrence networks

A long-standing question in community ecology is what determines the identity of species that coexist across local communities or metacommunity assembly. To shed light upon this question, we used a network approach to analyse the drivers of species co-occurrence patterns. In particular, we focus on the potential roles of body size and trophic status as determinants of metacommunity cohesion because of their link to resource use and dispersal ability. Small-sized individuals at low-trophic levels, and with limited dispersal potential, are expected to form highly linked subgroups, whereas large-size individuals at higher trophic positions, and with good dispersal potential, will foster the spatial coupling of subgroups and the cohesion of the whole metacommunity. By using modularity analysis, we identified six modules of species with similar responses to ecological conditions and high co-occurrence across local communities. Most species either co-occur with species from a single module or are connectors of the whole network. Among the latter are carnivorous species of intermediate body size, which by virtue of their high incidence provide connectivity to otherwise isolated communities playing the role of spatial couplers. Our study also demonstrates that the incorporation of network tools to the analysis of metacommunity ecology can help unveil the mechanisms underlying patterns and processes in metacommunity assembly.
Are clinical parameters and biomarkers predictive of severity of acute pulmonary emboli on CTPA?

BACKGROUND Previous studies have shown that findings of computed tomography pulmonary angiography (CTPA) relate to outcome in pulmonary embolus (PE). These include clot burden as quantified using an obstruction index and markers of pressure overload such as right ventricle to left ventricle size ratio (RV/LV ratio). Little data exists correlating these findings with clinical presentation and biomarkers. AIM To explore the link between clinical presentation and biomarkers with CTPA findings. METHODS Retrospective case note analysis of consecutive cases presenting to a large teaching hospital. An independent radiologist reviewed CTPAs and clot burden quantified using an obstruction index. RESULTS One hundred and seventy cases were identified and notes retrieved in 137 cases. (i) CLINICAL PRESENTATION correlation was seen between clot burden and systolic blood pressure (BP) (r = -0.299, P = 0.0006) and heart rate (r = 0.240, P = 0.0056). Median obstruction index was significantly higher in those with a presenting BP <90 mmHg [41.25% (95% CI 30-50) vs. 15% (95% CI 12.5-25), (P = 0.0004)]. Clot burden was significantly higher in patients with temperature of >37.5 degrees C [30% (95% CI 25.0-42.5) vs. 15% (95% CI 12.5-28.3), P = 0.02)] and (ii)Biomarkers: significant correlation between clot burden and D-dimer was seen (r = 0.36, P = 0.0001). Location of thrombus was associated with significant differences in D-dimer level. A subgroup of patients had cardiac biomarkers measured (n = 24). There was a statistically significant correlation between troponin I and clot burden (r = 0.412, P = 0.048) and RV/LV ratio (r = 0.699, P = 0.0013). DISCUSSION These findings suggest that clinical parameters and biomarkers have a role in predicting the radiological severity of PE. These data support the need for further studies of risk stratification in patients presenting with acute PE.
The functional role of microRNA in acute lymphoblastic leukemia: relevance for diagnosis, differential diagnosis, prognosis, and therapy

MicroRNAs (miRNAs), a new class of noncoding RNAs, which can hybridize to target messenger RNAs and regulate their expression posttranscriptionally, express differentially in distinct stages of lymphopoiesis and influence the direction of lymphoid precursor maturation. Hence, there is aberrant expression of miRNAs involved in malignant lymphopoiesis, and these aberrations can be used as signatures of acute lymphoblastic leukemia (ALL) with different subtypes. In addition, changes in the expression of several miRNAs may have functional relevance with leukemogenesis or drug resistance. As a result, the reversal of the expression of these miRNAs may alleviate the disease to some extent and improve clinical outcomes. However, among the studies of miRNAs, there are still some problems that need to be solved to understand the function of miRNAs in ALL more thoroughly.
Compiler-Driven Software Speculation for Thread-Level Parallelism

Current parallelizing compilers can tackle applications exercising regular access patterns on arrays or affine indices, where data dependencies can be expressed in a linear form. Unfortunately, there are cases that independence between statements of code cannot be guaranteed and thus the compiler conservatively produces sequential code. Programs that involve extensive pointer use, irregular access patterns, and loops with unknown number of iterations are examples of such cases. This limits the extraction of parallelism in cases where dependencies are rarely or never triggered at runtime. Speculative parallelism refers to methods employed during program execution that aim to produce a valid parallel execution schedule for programs immune to static parallelization. The motivation for this article is to review recent developments in the area of compiler-driven software speculation for thread-level parallelism and how they came about. The article is divided into two parts. In the first part the fundamentals of speculative parallelization for thread-level parallelism are explained along with a design choice categorization for implementing such systems. Design choices include the ways speculative data is handled, how data dependence violations are detected and resolved, how the correct data are made visible to other threads, or how speculative threads are scheduled. The second part is structured around those design choices providing the advances and trends in the literature with reference to key developments in the area. Although the focus of the article is in software speculative parallelization, a section is dedicated for providing the interested reader with pointers and references for exploring similar topics such as hardware thread-level speculation, transactional memory, and automatic parallelization.
A General Agnostic Active Learning Algorithm

We present an agnostic active learning algorithm for any hypothesis class of bounded VC dimension under arbitrary data distributions. Most previous work on active learning either makes strong distributional assumptions, or else is computationally prohibitive. Our algorithm extends the simple scheme of Cohn, Atlas, and Ladner [1] to the agnostic setting, using reductions to supervised learning that harness generalization bounds in a simple but subtle manner. We provide a fall-back guarantee that bounds the algorithm's label complexity by the agnostic PAC sample complexity. Our analysis yields asymptotic label complexity improvements for certain hypothesis classes and distributions. We also demonstrate improvements experimentally.
Music Therapy with Bereaved Youth: Expressing Grief and Feeling Better.

The use of music for tberapeutic purposes has been reported for many centuries, from the biblical tales of David soothing King Saul with his harp, to the healing rituals of indigenous cultures. Today, the advent of MP3 players and other new technologies has extended possibilities for self-care through music since it is now feasible to listen to preferred tracks anywhere and anytime. An investigation of how adults use MP3 listening devices revealed that music affords immediate opportunities to regulate mood, access emotions, adjust energy levels, and create boundaries around oneself in public places (Skâniand, 2010). Other investigations have described the ways adults use personally significant songs to connect to the past and reintegrate different aspects of themselves in the present (DeNora, 2000). These everyday self-care strategies have led to descriptions of music as a "technology of health" (Ruud, 2010) that has potential for belping those with "health" problems. This potential has been confirmed in a study of Norwegian adults with chronic illness who required minimal encouragement to begin using music as "self-therapy," with participants creating personal musical rituals that provided a structure and focus for health-oriented experiences (Batt-Rawden, DeNora, & Ruud, 2005).
Recombinant human activated protein C attenuates the inflammatory response in endothelium and monocytes by modulating nuclear factor-&kgr;B

ObjectiveTo review the anti-inflammatory and anti-apoptotic properties of drotrecogin alfa (activated) (recombinant human activated protein C), emphasizing its modulatory effects on endothelial nuclear factor-&kgr;B. We propose a broad anti-inflammatory effect of drotrecogin alfa (activated), acting on both endothelium and monocytes. Data SourcesA selected review of the published literature on nuclear factor-&kgr;B, severe sepsis, and the use of drotrecogin alfa (activated) in clinical and preclinical models, together with data derived from preclinical gene profiling of model systems. Data Extraction and SynthesisData from the PROWESS trial support the preclinical evidence of an antithrombotic effect of drotrecogin alfa (activated). Anti-inflammatory effects through reduction of thrombin generation and through thrombin-independent mechanisms in mononuclear and endothelial cells are reviewed. Inhibition of apoptosis is used as an example of the protective effect of drotrecogin alfa (activated) on endothelial and mononuclear cell dysfunction. ConclusionsDrotrecogin alfa (activated) acts as a modulator of nuclear factor-&kgr;B to aid in the host immune response in endothelium and monocytes. Extrapolation of gene array findings to explain apoptosis in endothelium and monocytes, coupled with emerging preclinical reports, provides evidence to support the role of drotrecogin alfa (activated) in modulating nuclear factor-&kgr;B.
Discrimination and Retrieval of Environmental Sounds

The human auditory sense may be regarded as the second most important sense after the sense of sight. This valuation is reflected in the field of information retrieval where until recently research concentrated on visual information retrieval. Even research in audio retrieval (AR) focused on one single aspect of hearing, namely understanding of speech. With the upcoming of large music databases in recent years, a second area of AR gained importance: music information retrieval (MIR). The goal of MIR is to enable efficient search and retrieval in the music databases mentioned above. The latest research area in the domain of audio retrieval is the retrieval of environmental sounds. One may argue that environmental sound retrieval deserves a more prominent role than it has. Most sounds humans hear are neither speech nor music but various environmental sounds. By incorporating environmental sounds into retrieval systems, a vast amount of additional information becomes available. In this thesis the applicability of a range of audio features in the domain of environmental sound retrieval is investigated. Furthermore state-of-the-art techniques in audio retrieval are identified by a broad survey of relevant literature covering all three areas of AR (speech, music, and environmental sounds). The quality of the features is examined with three different classification techniques. Finally, a set of novel audio features, developed by the author, is compared to established features. Results indicate that further research is necessary. There is particularly a lack of low-dimensional and computationally cheap audio descriptors suitable for the use in environmental sound retrieval.
Synaptic Targeting of Double-Projecting Ventral CA1 Hippocampal Neurons to the Medial Prefrontal Cortex and Basal Amygdala

The acquisition and retrieval of contextual fear memory requires coordinated neural activity in the hippocampus, medial prefrontal cortex (mPFC), and amygdala. The contextual information encoded in the hippocampus is conveyed to the mPFC and amygdala for contextual fear conditioning. Previous studies have suggested that a CA1 neuronal population in the ventral hippocampus (VH) projects to both the mPFC and amygdala and is recruited in context-dependent control of conditioned fear. However, how double-projecting ventral CA1 hippocampal (vCA1) neurons modulate the activity of the mPFC and amygdala at the synaptic level has not been determined previously. Here, we show that the optogenetic silencing of the VH prevented the recall of contextual fear memory in mice, indicating its role in contextual fear expression. In dual retrograde viral tracing and c-Fos immunostaining experiments, we found that a proportion of vCA1 neurons projected to both the mPFC and amygdala and were recruited preferentially during context exposure, suggesting their role in encoding context representations. Moreover, optogenetic stimulation of axon collaterals of double-projecting vCA1 neurons induced monosynaptic excitatory responses in both the mPFC and basal amygdala, indicating that they could convey contextual information through the VH–mPFC and VH–amygdala pathways. The activation of double-projecting vCA1 neurons also induced action potential firings in the mPFC neurons that project to the amygdala, suggesting that they can also activate the VH–mPFC–amygdala pathway. With these synaptic mechanisms, double-projecting vCA1 neurons could induce synchronized neural activity in the mPFC and amygdala and convey contextual information efficiently to the basal amygdala for contextual fear conditioning. SIGNIFICANCE STATEMENT This work demonstrates that ventral CA1 hippocampal (vCA1) neurons projecting to both the medial prefrontal cortex (mPFC) and amygdala are activated preferentially when contextual information is processed in the ventral hippocampus, which is required for contextual fear expression. Our electrophysiological experiments reveal that the activation of double-projecting vCA1 neurons induces excitatory synaptic activity in both the mPFC and amygdala. These results suggest that double-projecting vCA1 neurons could contribute to contextual fear responses by inducing synchronized activity in the mPFC and amygdala and conveying contextual information to the basal amygdala more efficiently than vCA1 neurons projecting to either the mPFC or amygdala alone. These findings provide important insights into the mechanisms of the acquisition and retrieval of contextual fear memory.
Distributed testing against independence with multiple terminals

Motivated by distributed learning with Big Data sets problems, we study a distributed testing against independence problem with multiple terminals. We connect the problem at hand to a source coding with multiple helpers problem, which is open in general. We fully characterize the rate region of the source coding with multiple helpers problem under a certain Markovian condition. Using this rate region characterization, we obtain a single-letter characterization of the optimal error exponent for the type 2 error probability under the type 1 error probability and communication rates constraints.
Diabetes-Resistant NOR Mice Are More Severely Affected by Streptozotocin Compared to the Diabetes-Prone NOD Mice: Correlations with Liver and Kidney GLUT2 Expressions

Nonobese Diabetic (NOD) mice are susceptible strains for Type 1 diabetes development, and Nonobese Diabetes-Resistant (NOR) mice are defined as suitable controls for NOD mice in non-MHC-related research. Diabetes is often accelerated in NOD mice via Streptozotocin (STZ). STZ is taken inside cells via GLUT2 transmembrane carrier proteins, the major glucose transporter isoforms in pancreatic beta cells, liver, kidneys, and the small intestine. We observed severe adverse effects in NOR mice treated with STZ compared to NOD mice that were made diabetic with a similar dose. We suggested that the underlying mechanism could be differential GLUT2 expressions in pancreatic beta cells, yet immunofluorescent and immunohistochemical studies revealed similar GLUT2 expression levels. We also detected GLUT2 expression profiles in NOD and NOR hepatic and renal tissues by western blot analysis and observed considerably higher GLUT2 expression levels in liver and kidney tissues of NOR mice. Although beta cell GLUT2 expression levels are frequently evaluated as a marker predicting STZ sensitivity in animal models, we report here very different diabetic responses to STZ in two different animal strains, in spite of similar initial GLUT2 expressions in beta cells. Furthermore, use of NOR mice in STZ-mediated experimental diabetes settings should be considered accordingly.
The influence of demographic processes on the transformation of Đakovština

U posljednjem stoljecu doslo je do velikih demogeografskih i gospodarskih promjena koje su snažno utjecale na transformaciju kulturnog pejsaža Đakovstine. Demogeografske promjene su jasno vidljive i odnose se na smanjenje ukupnog broja stanovnika, gustoce te na daljnje pogorsanje razmjestaja, prirodnog kretanja i migracije, kao i negativne promjene u strukturnim obilježjima stanovnistva. Depopulacija je dominantan proces, a sadasnje drustveno-gospodarsko stanje ne pruža mogucnosti skore i brze demografske te ukupne drustveno-gospodarske revitalizacije ovog dijela Hrvatske.
Changes in Soybean Global Gene Expression after Application of Lipo-Chitooligosaccharide from Bradyrhizobium japonicum under Sub-Optimal Temperature

Lipo-chitooligosaccharides (LCOs), signal compounds produced by N2-fixing rhizobacteria after isoflavone induction, initiate nodule formation in host legumes. Given LCOs' structural similarity to pathogen-response-eliciting chitin oligomers, foliar application of LCOs was tested for ability to induce stress-related genes under optimal growth conditions. In order to study the effects of LCO foliar spray under stressed conditions, soybean (Glycine max) seedlings grown at optimal temperature were transferred to sub-optimal temperature. After a 5-day acclimation period, the first trifoliate leaves were sprayed with 10−7 M LCO (NodBj-V (C18∶1, MeFuc)) purified from genistein-induced Bradyrhizobium japonicum culture, and harvested at 0 and 48 h following treatment. Microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays. Compared to the control at 48 h after LCO treatment, a total of 147 genes were differentially expressed as a result of LCO treatment, including a number of stress-related genes and transcription factors. In addition, during the 48 h time period following foliar spray application, over a thousand genes exhibited differential expression, including hundreds of those specific to the LCO-treated plants. Our results indicated that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment. Quantitative real-time PCR (qPCR) validated the microarray data.
A Robust Hierarchical Clustering Algorithm and its Application in 3D Model Retrieval

Clustering techniques can be adopted to analyze 3D model database and improve the retrieval performance. However, 3D model database lack valuable prior knowledge. Thus, it becomes difficult for the clustering methods to pre-decide the appropriate parameter's value. Moreover, clustering methods are short at handling outliers by treating outliers as "noise". The paper introduces a robust hierarchical clustering algorithm for analyzing 3D model database. The proposed algorithm stops automatically by utilizing outlier information and adopts the concept of core group to reduce the influence of parameter on the clustering result. Core group refers to the data that are always clustered together. After discussing some desirable properties of the new algorithm, the paper conducts a series of experiments on Princeton shape benchmark and 2 real-life datasets from UCI. Comparative study demonstrates advantages of our algorithm
Innate secretory antibodies protect against natural Salmonella typhimurium infection

The production of IgA is induced in an antigen-unspecific manner by commensal flora. These secretory antibodies (SAbs) may bind multiple antigens and are thought to eliminate commensal bacteria and self-antigens to avoid systemic recognition. In this study, we addressed the role of “innate” SAbs, i.e., those that are continuously produced in normal individuals, in protection against infection of the gastrointestinal tract. We used polymeric immunoglobulin receptor (pIgR−/−) knock-out mice, which are unable to bind and actively transport dimeric IgA and pentameric IgM to the mucosae, and examined the role of innate SAbs in protection against the invasive pathogen Salmonella typhimurium. In vitro experiments suggested that innate IgA in pIgR−/− serum bound S. typhimurium in a cross-reactive manner which inhibited epithelial cell invasion. Using a “natural” infection model, we demonstrated that pIgR−/− mice are profoundly sensitive to infection with S. typhimurium via the fecal-oral route and, moreover, shed more bacteria that readily infected other animals. These results imply an important evolutionary role for innate SAbs in protecting both the individual and the herd against infections, and suggest that the major role of SAbs may be to prevent the spread of microbial pathogens throughout the population, rather than protection of local mucosal surfaces.