Miracle-dz/UniFAR-FTUs huggingface dataset:
Suppressor mutations in rpoA suggest that OmpR controls transcription by direct interaction with the alpha subunit of RNA polymerase

We have isolated mutations in rpoA, the gene encoding the alpha subunit of RNA polymerase, that specifically affect transcriptional control by OmpR and EnvZ, the two-component regulatory system that controls porin gene expression in Escherichia coli. Characterization of these mutations and a previously isolated rpoA allele suggests that both positive and negative regulation of porin gene transcription involves a direct interaction between OmpR and RNA polymerase through the alpha subunit. Several of the rpoA mutations cluster in the carboxy-terminal portion of the alpha protein, further suggesting that it is this domain of alpha that is involved in interaction with OmpR and perhaps other transcriptional regulators as well.
Fabrication of Biomimetic and Bioinspired Membranes

Biomimetic and bioinspired membranes are those membranes that are fabricated with natural or natural-like (inorganic, organic, or hybrid) materials via biomimetic and bioinspired approaches (bio-mineralization, bio-adhesion, self-assembly, etc.) to tailor-specific properties (sophisticated structures, hierarchical organizations, controlled selectivity, antifouling or self-cleaning properties, etc.). With the support of knowledge on mechanisms, models and functions from many scientific disciplines, research activity on biomimetic and bioinspired membrane during the last decade has increased rapidly.
Effects of Cyclic Increase in Gonadotropins on the In Vitro Development of Primordial Follicles to Antral Stage

The aim of this study was to evaluate the effects of FSH and LH on follicle development during a long-term culture of cryopreserved human ovarian tissue, using morphological and ultrastructural examinations. Thawed ovarian tissue slices from a 4-year-old child with Wilms tumor were cultured for 32 weeks in two different culture conditions, without (medium A) and with (medium B) a monthly peaked increase in FSH and LH. At week 32, in the medium B cultured tissue, a cluster of preantral follicles associated with two oocytes prematurely ovulated was observed, suggesting that the cyclic increase of gonadotropins promoted thawed follicles to grow up to the antral stage. However, the integrity and coordinated follicle development were not maintained. Indeed, ultrastructural analysis showed a well-preserved “naked” oocyte with concomitant features of immaturity and maturity, as if this culture condition had led to an asynchronous maturation of oocyte cytoplasmic components.
Nurse staffing and inpatient hospital mortality.

BACKGROUND Cross-sectional studies of hospital-level administrative data have shown an association between lower levels of staffing of registered nurses (RNs) and increased patient mortality. However, such studies have been criticized because they have not shown a direct link between the level of staffing and individual patient experiences and have not included sufficient statistical controls. METHODS We used data from a large tertiary academic medical center involving 197,961 admissions and 176,696 nursing shifts of 8 hours each in 43 hospital units to examine the association between mortality and patient exposure to nursing shifts during which staffing by RNs was 8 hours or more below the staffing target. We also examined the association between mortality and high patient turnover owing to admissions, transfers, and discharges. We used Cox proportional-hazards models in the analyses with adjustment for characteristics of patients and hospital units. RESULTS Staffing by RNs was within 8 hours of the target level for 84% of shifts, and patient turnover was within 1 SD of the day-shift mean for 93% of shifts. Overall mortality was 61% of the expected rate for similar patients on the basis of modified diagnosis-related groups. There was a significant association between increased mortality and increased exposure to unit shifts during which staffing by RNs was 8 hours or more below the target level (hazard ratio per shift 8 hours or more below target, 1.02; 95% confidence interval [CI], 1.01 to 1.03; P<0.001). The association between increased mortality and high patient turnover was also significant (hazard ratio per high-turnover shift, 1.04; 95% CI, 1.02 to 1.06; P<0.001). CONCLUSIONS In this retrospective observational study, staffing of RNs below target levels was associated with increased mortality, which reinforces the need to match staffing with patients' needs for nursing care. (Funded by the Agency for Healthcare Research and Quality.).
SimBioNeT: A Simulator of Biological Network Topology

Studying biological networks at topological level is a major issue in computational biology studies and simulation is often used in this context, either to assess reverse engineering algorithms or to investigate how topological properties depend on network parameters. In both contexts, it is desirable for a topology simulator to reproduce the current knowledge on biological networks, to be able to generate a number of networks with the same properties and to be flexible with respect to the possibility to mimic networks of different organisms. We propose a biological network topology simulator, SimBioNeT, in which module structures of different type and size are replicated at different level of network organization and interconnected, so to obtain the desired degree distribution, e.g., scale free, and a clustering coefficient constant with the number of nodes in the network, a typical characteristic of biological networks. Empirical assessment of the ability of the simulator to reproduce characteristic properties of biological network and comparison with E. coli and S. cerevisiae transcriptional networks demonstrates the effectiveness of our proposal.
Pattern Formation in Electrical Exploding of Thin Metal Films

We present the experimental results of the nanometer Zn films electrical explosion in the air. The film destruction is accompanied with the stratification; the strata are formed in the transverse direction to the applied electric field. The initial strata growth can be explained by the electro-thermal instability development. The strata propagation velocity reaches 50 km/s and depends on the current. The pattern is formed during ~60 ns and each stratum's voltage settles at the constant level limited by arc discharges. We found that strata fractal dimension D=1.55±0.02 for all experiments, which means that the patterns are determined by a certain universal mechanism.
Utility of MRI Diffusion Techniques in the Evaluation of Tumors of the Head and Neck

The use of diffusion-weighted imaging in the head and neck is an increasingly used technique that requires adaptation of the acquisition parameters. Parallel imaging and emerging techniques such as IVIM are playing a new role. The main indications for performing DWI are tissue characterization, nodal staging and therapy monitoring. Lower apparent diffusion coefficients have been reported in this region for malignant lesions such as SCC, lymphoma and metastatic lymph node, as opposed to higher ADC in benign lesions and lymph nodes. Follow-up and early response to treatment are reflected in an ADC increase in both primary tumor and nodal metastasis.
Towards fast running: Open-loop speed and direction control of a single-legged hopper

Traditional 2D single-legged hoppers were able to demonstrate stable bi-directional running in a closed-loop approach. In contrast, we employ an open-loop control to achieve high-speed (≈0.8 m/sec or 1.78 mph) bi-directional dynamic running of the reconfigurable leg length hopper (RLLH). Our hopper has variable linear joint in series with a passive spring that allows changing its effective leg length in realtime. Furthermore by instantaneously changing the leg length at a particular amplitude and frequency. The required “thrust-forces” can be produced. We hypothesize that the direction and the speed of our hopper can be smoothly controlled by only changing the phase of the thrust-forces being applied to the ground, i.e., the change in phase between the leg-reconfiguration and the leg-oscillation. This is experimentally evaluated by varying the phase of leg-reconfiguration up-to the range of 0-2π rad (0-360 deg). Our results show a large region of a symmetric running. Moreover, a novel gait called “in-place running1” is found, where the speed of running is zero. We demonstrate that by only altering the phase of applying thrust-forces together with a constant leg oscillation can robustly control the speed and transition in the direction of locomotion.
Estimation of the acoustic properties of the nasal tract during the production of nasalized vowels

Accurate estimation of velar movements is useful for automatic speech recognition, speech enhancement, and diagnosis of certain speech disorders. This paper reports on initial results of a project on estimation of velar movements, for two-microphone setups where the microphones are differentially positioned to pick up nasal and oral speech output. Toward this goal, we propose a method that allows detailed estimation of the acoustic properties of the nasal tract in the simplified condition where the two microphone signals exhibit complete source separation. We successfully test the method against synthetic speech, generated by an articulatory synthesizer in which the acoustic properties of the simulated nasal tract are known.
Fates beyond traits: ecological consequences of human-induced trait change

Human‐induced trait change has been documented in freshwater, marine, and terrestrial ecosystems worldwide. These trait changes are driven by phenotypic plasticity and contemporary evolution. While efforts to manage human‐induced trait change are beginning to receive some attention, managing its ecological consequences has received virtually none. Recent work suggests that contemporary trait change can have important effects on the dynamics of populations, communities, and ecosystems. Therefore, trait changes caused by human activity may be shaping ecological dynamics on a global scale. We present evidence for important ecological effects associated with human‐induced trait change in a variety of study systems. These effects can occur over large spatial scales and impact system‐wide processes such as trophic cascades. Importantly, the magnitude of these effects can be on par with those of traditional ecological drivers such as species presence. However, phenotypic change is not always an agent of ecological change; it can also buffer ecosystems against change. Determining the conditions under which phenotypic change may promote vs prevent ecological change should be a top research priority.
Anti-Müllerian hormone levels in peripubertal daughters of women with polycystic ovary syndrome.

CONTEXT We have previously observed increased anti-Müllerian hormone (AMH) levels in prepubertal daughters of polycystic ovary syndrome (PCOS) women, suggesting that these girls may have an altered follicular development. However, it is not known whether AMH levels remain increased during puberty. OBJECTIVE The aim was to establish whether the increased AMH levels observed in prepubertal daughters of PCOS women persist during the peripubertal period, a stage during which the gonadal axis is activated and PCOS may become clinically manifested. DESIGN We studied 28 daughters (8-16 yr old) of PCOS women (PCOSd) and 33 daughters (8-16 yr old) of control women (Cd). In both groups, an oral glucose tolerance test was performed. Gonadotropins, sex hormones, and AMH were determined in a fasting sample. RESULTS Both groups were comparable in age, body mass index, and breast Tanner stage. Free androgen index, testosterone, AMH (Cd 14.4 +/- 8.0 pM vs. PCOSd 24.0 +/- 19.0 pM; P = 0.012), and 2-h insulin levels were significantly higher in the PCOSd group compared with the control group. The average ovarian volume was significantly higher in the PCOSd group. In both groups a positive correlation between 2-h insulin and AMH concentrations was observed (PCOSd: r = 0.530, P = 0.007; Cd: r =0.561, P = 0.008). CONCLUSIONS AMH concentrations are increased in peripubertal PCOSd. These findings, along with the results of our previous study, suggest that PCOSd appear to show an increased follicular mass that is established during early development, and persists during puberty.
Power calculation for overall hypothesis testing with high‐dimensional commensurate outcomes

The complexity of system biology means that any metabolic, genetic, or proteomic pathway typically includes so many components (e.g., molecules) that statistical methods specialized for overall testing of high‐dimensional and commensurate outcomes are required. While many overall tests have been proposed, very few have power and sample size methods. We develop accurate power and sample size methods and software to facilitate study planning for high‐dimensional pathway analysis. With an account of any complex correlation structure between high‐dimensional outcomes, the new methods allow power calculation even when the sample size is less than the number of variables. We derive the exact (finite‐sample) and approximate non‐null distributions of the ‘univariate’ approach to repeated measures test statistic, as well as power‐equivalent scenarios useful to generalize our numerical evaluations. Extensive simulations of group comparisons support the accuracy of the approximations even when the ratio of number of variables to sample size is large. We derive a minimum set of constants and parameters sufficient and practical for power calculation. Using the new methods and specifying the minimum set to determine power for a study of metabolic consequences of vitamin B6 deficiency helps illustrate the practical value of the new results. Free software implementing the power and sample size methods applies to a wide range of designs, including one group pre‐intervention and post‐intervention comparisons, multiple parallel group comparisons with one‐way or factorial designs, and the adjustment and evaluation of covariate effects. Copyright © 2013 John Wiley & Sons, Ltd.
Effective Use of Textbooks: A Neglected Aspect of Education in Pakistan

Given the significant role that textbooks play in many countries of the developing world, the paper highlights issues related to the use of the textbook in rural Pakistan, and identifies ways to improve upon current practices. The findings presented in this paper emerge from our analysis of teachers’ experiences and practices related to the use of Science textbooks in public schools. Since the existing knowledge base is limited on teachers’ actual use of the textbook, the paper attempts to fill in this gap by highlighting the various issues related to teachers’ perceptions and practices. These include teachers’ limited use of textbooks, access to textbooks, information gaps and limitations of textbooks – all working to restrict the use of the textbook as a learning resource. The paper concludes by offering recommendations on improving textbook usage in Pakistan.
Anopheles gambiae Immune Responses to Human and Rodent Plasmodium Parasite Species

Transmission of malaria is dependent on the successful completion of the Plasmodium lifecycle in the Anopheles vector. Major obstacles are encountered in the midgut tissue, where most parasites are killed by the mosquito's immune system. In the present study, DNA microarray analyses have been used to compare Anopheles gambiae responses to invasion of the midgut epithelium by the ookinete stage of the human pathogen Plasmodium falciparum and the rodent experimental model pathogen P. berghei. Invasion by P. berghei had a more profound impact on the mosquito transcriptome, including a variety of functional gene classes, while P. falciparum elicited a broader immune response at the gene transcript level. Ingestion of human malaria-infected blood lacking invasive ookinetes also induced a variety of immune genes, including several anti-Plasmodium factors. Twelve selected genes were assessed for effect on infection with both parasite species and bacteria using RNAi gene silencing assays, and seven of these genes were found to influence mosquito resistance to both parasite species. An MD2-like receptor, AgMDL1, and an immunolectin, FBN39, showed specificity in regulating only resistance to P. falciparum, while the antimicrobial peptide gambicin and a novel putative short secreted peptide, IRSP5, were more specific for defense against the rodent parasite P. berghei. While all the genes that affected Plasmodium development also influenced mosquito resistance to bacterial infection, four of the antimicrobial genes had no effect on Plasmodium development. Our study shows that the impact of P. falciparum and P. berghei infection on A. gambiae biology at the gene transcript level is quite diverse, and the defense against the two Plasmodium species is mediated by antimicrobial factors with both universal and Plasmodium-species specific activities. Furthermore, our data indicate that the mosquito is capable of sensing infected blood constituents in the absence of invading ookinetes, thereby inducing anti-Plasmodium immune responses.
Recruitment of RNA polymerase II cofactor PC4 to DNA damage sites

The multifunctional nuclear protein positive cofactor 4 (PC4) is involved in various cellular processes including transcription, replication, and chromatin organization. Recently, PC4 has been identified as a suppressor of oxidative mutagenesis in Escherichia coli and Saccharomyces cerevisiae. To investigate a potential role of PC4 in mammalian DNA repair, we used a combination of live cell microscopy, microirradiation, and fluorescence recovery after photobleaching analysis. We found a clear accumulation of endogenous PC4 at DNA damage sites introduced by either chemical agents or laser microirradiation. Using fluorescent fusion proteins and specific mutants, we demonstrated that the rapid recruitment of PC4 to laser-induced DNA damage sites is independent of poly(ADP-ribosyl)ation and γH2AX but depends on its single strand binding capacity. Furthermore, PC4 showed a high turnover at DNA damages sites compared with the repair factors replication protein A and proliferating cell nuclear antigen. We propose that PC4 plays a role in the early response to DNA damage by recognizing single-stranded DNA and may thus initiate or facilitate the subsequent steps of DNA repair.
A Cognitive Account of the Lexical Polysemy of Chinese Kai

Graduate Institute of English, National Taiwan Normal University Abstract Since polysemy has multiple but related senses, finding any coherent system would seem impossible. But its senses are not random. When we look at inferences among them, it becomes clear that there must be a systematic structure of some kind. Based on the prototype theory, which views lexical items as constituting natural categories of senses, the present work aims at proposing solutions to problems resulting from the polysemy of kai. After an in-depth analysis of the polysemy kai, we find that the links between polysemy senses are defined not only by shared properties (i.e. analogy), but also by conceptual connections (e.g. metonymy or metaphor). This study suggests that polysemy reflects human's categorization of things and can be successfully accounted for by a cognitive approach.
Generation of time delays: Simplified models of intracellular signalling in cerebellar Purkinje cells

In many neuronal systems, information is encoded in temporal spike patterns. The recognition and storage of temporal patterns requires the generation and modulation of time delays between inputs and outputs. In cerebellar Purkinje cells, stimulation of metabotropic glutamate receptors (mGluRs) results in a delayed calcium and voltage response that has been implicated in classical conditioning and temporal pattern recognition. Here, we analyse and simplify a complex model of the intracellular signalling network that has been proposed as a substrate for this delayed response. We systematically simplify the original model, present a minimal model of time delay generation, and show that a delayed response can be produced by the combination of negative feedback and autocatalysis, without any intervening signalling steps that would contribute additive delays. The minimal model is analysed using phase plane methods, and classified as an excitable system. We discuss the implication of excitability for computations performed by intracellular signalling networks in general.
Fuzzy classification-based emotional context recognition from online social networks messages

Over the past several years, social networking services or micro-blogs have become ubiquitously accessible anytime and contain users' opinions expressed in the form of short text messages. In this paper, we introduce a new automatic approach named FEmoRec for emotional context recognition from online social networks that applies a semantic similarity measure based on Multi-Layer Perceptron Neural Net Model. We rely on the assumption that a tweet may belong to many emotional categories with different membership degrees. We classify the tweet by computing an emotion vector that represents the tweet's fuzzy membership values to Ekman's emotion classes. Carried out experiments emphasize the relevance of our proposal, compared to other methods.
The Drosophila GAGA Factor Is Required for Dosage Compensation in Males and for the Formation of the Male-Specific-Lethal Complex Chromatin Entry Site at 12DE

Drosophila melanogaster males have one X chromosome, while females have two. To compensate for the resulting disparity in X-linked gene expression between the two sexes, most genes from the male X chromosome are hyperactivated by a special dosage compensation system. Dosage compensation is achieved by a complex of at least six proteins and two noncoding RNAs that specifically associate with the male X. A central question is how the X chromosome is recognized. According to a current model, complexes initially assemble at ∼35 chromatin entry sites on the X and then spread bidirectionally along the chromosome where they occupy hundreds of sites. Here, we report that mutations in Trithorax-like (Trl) lead to the loss of a single chromatin entry site on the X, male lethality, and mislocalization of dosage compensation complexes.
A Petri net meta-model to develop software components for embedded systems

This paper presents a new Petri net (PN) meta-model, called shobi-PN v2.0, that can be used to specify, the dynamic behaviour of concurrent systems, using object-oriented modelling concepts together with a generalised arc set capable of coping with the complexity of the current embedded systems. This new Petri net meta-model can also be used to support a component-based development approach in the design of generic and parametrisable control-oriented software components for embedded systems.
Term Structure Models Driven by General Lévy Processes

As a generalization of the Gaussian Heath–Jarrow–Morton term structure model, we present a new class of bond price models that can be driven by a wide range of Lévy processes. We deduce the forward and short rate processes implied by this model and prove that, under certain assumptions, the short rate is Markovian if and only if the volatility structure has either the Vasicek or the Ho–Lee form. Finally, we compare numerically forward rates and European call option prices in a model driven by a hyperbolic Lévy motion with those in the Gaussian model.