Miracle-dz/UniFAR-FTUs huggingface dataset:
Keratinocyte growth factor-2 intratracheal instillation significantly attenuates ventilator-induced lung injury in rats

Preservation or restoration of normal alveolar epithelial barrier function is crucial for pulmonary oedema resolution. Keratinocyte growth factor‐2 (KGF‐2), a potent epithelial cell mitogen, may have a role in preventing ventilator‐induced lung injury (VILI), which occurs frequently in mechanically ventilated patients. The aim of the study was to test the role of KGF‐2 in VILI in rats. Forty healthy adult male Sprague‐Dawley rats were randomly allocated into four groups, where rats in Groups HVZP (high‐volume zero positive end‐expiratory pressure) and HVZP+KGF‐2 were given intratracheally equal PBS and 5 mg/kg KGF‐2 72 hrs before 4 hrs HVZP ventilation (20 ml/kg), respectively, while PBS and KGF‐2 were administered in the same manner in Groups Control and KGF‐2, which underwent tracheotomy only with spontaneous breathing. Inflammatory cytokines (tumour necrosis factor‐α, macrophage inflammatory protein 2), neutrophil and total protein levels in bronchoalveolar lavage fluid and surfactant protein mRNA expression in lung tissue were detected; the number of alveolar type II cells, lung water content and lung morphology were also evaluated. The results indicate that pre‐treatment with KGF‐2 showed dramatic improvement in lung oedema and inflammation compared with HVZP alone, together with increased surfactant protein mRNA and alveolar type II cells. Our results suggest that KGF‐2 might be considered a promising prevention for human VILI or other acute lung injury diseases.
Evidence for a role of transmembrane protein p25 in localization of protein tyrosine phosphatase TC48 to the ER

T-cell protein tyrosine phosphatase gives rise to two splice isoforms: TC48, which is localized to the endoplasmic reticulum (ER) and TC45, a nuclear protein. The present study was undertaken to identify proteins that are involved in targeting TC48 to the ER. We identified two TC48-interacting proteins, p25 and p23, from a yeast two-hybrid screen. p23 and p25 are members of a family of putative cargo receptors that are important for vesicular trafficking between Golgi complex and ER. Both p23 and p25 associate with overexpressed TC48 in Cos-1 cells as determined by coimmunoprecipitation. A significant amount of TC48 colocalized initially with ERGIC and Golgi complex markers (in addition to ER and nuclear membrane localization) and was then retrieved to the ER. Coexpression with p25 enhanced ER localization of TC48, whereas coexpression with p23 resulted in its trapping in membranous structures. Coexpression of a p25 mutant lacking the ER-localization signal KKxx resulted in enhanced Golgi localization of TC48. Forty C-terminal amino acid residues of TC48 (position 376-415) were sufficient for interaction with p23 (but not with p25) and targeted green fluorescence protein (GFP) to the Golgi complex. Targeting of GFP to the ER required 66 C-terminal amino acid residues of TC48 (position 350-415), which showed interaction with p25 and p23. We suggest that TC48 translocates to the Golgi complex along the secretory pathway, whereas its ER localization is maintained by selective retrieval enabled by interactions with p25 and p23.
A novel bio-inspired predictive model for spam filtering based on dendritic cell algorithm

Electronic mail has become the most popular, frequently-used and powerful medium for quicker personal and business communications. However, one of the common security issues and annoying problems faced by email users and organizations is receiving a large number of unsolicited email messages, known as spam emails, every day. A traditional countermeasure in most email systems nowadays is simple filtering mechanisms that can block or quarantine unwanted emails based on some keywords defined by the user. These filters require continual effort to keep them relevant and current with some extensions proposed to improve their performance. However, due to the gigantic volumes of received emails and the continual change in spamming techniques to bypass the implemented solutions, novel automated ideas and countermeasures need to be investigated. This paper explores a novel algorithm inspired by the immune system called dendritic cell algorithm (DCA). This algorithm is evaluated on a number of benchmark datasets to detect spam emails. The results demonstrate that this approach can be a promising solution for email classification and spam filtering.
Zebrafish models of collagen VI-related myopathies

Collagen VI is an integral part of the skeletal muscle extracellular matrix, providing mechanical stability and facilitating matrix-dependent cell signaling. Mutations in collagen VI result in either Ullrich congenital muscular dystrophy (UCMD) or Bethlem myopathy (BM), with UCMD being clinically more severe. Recent studies demonstrating increased apoptosis and abnormal mitochondrial function in Col6a1 knockout mice and in human myoblasts have provided the first mechanistic insights into the pathophysiology of these diseases. However, how loss of collagen VI causes mitochondrial dysfunction remains to be understood. Progress is hindered in part by the lack of an adequate animal model for UCMD, as knockout mice have a mild motor phenotype. To further the understanding of these disorders, we have generated zebrafish models of the collagen VI myopathies. Morpholinos designed to exon 9 of col6a1 produced a severe muscle disease reminiscent of UCMD, while ones to exon 13 produced a milder phenotype similar to BM. UCMD-like zebrafish have increased cell death and abnormal mitochondria, which can be attenuated by treatment with the proton pump modifier cyclosporin A (CsA). CsA improved the motor deficits in UCMD-like zebrafish, but failed to reverse the sarcolemmal membrane damage. In all, we have successfully generated the first vertebrate model matching the clinical severity of UCMD and demonstrated that CsA provides phenotypic improvement, thus corroborating data from knockout mice supporting the use of mitochondrial permeability transition pore modifiers as therapeutics in patients, and providing proof of principle for the utility of the zebrafish as a powerful preclinical model.
LDPC codes for the Gaussian wiretap channel

A coding scheme for the Gaussian wiretap channel based on low-density parity-check (LDPC) codes is presented. The messages are transmitted over punctured bits to hide data from eavesdroppers. It is shown by means of density evolution that the BER of an eavesdropper, who operates below the code's SNR threshold and has the ability to use a bitwise MAP decoder, increases to 0.5 within a few dB. It is shown how asymptotically optimized LDPC codes can be designed with differential evolution where the goal is to achieve high reliability between friendly parties and security against a passive eavesdropper while keeping the security gap as small as possible. The proposed coding scheme is also efficiently encodable in almost linear time.
The OH (1720 MHz) Supernova Remnant Masers in W28: MERLIN and VLBA Polarization Observations

Full-polarization MERLIN and VLBA observations of the 1720 MHz maser emission from the OH molecule in the supernova remnant W28 are presented. Zeeman splitting (|| ≈ 0.75 mG) has been directly resolved between right- and left-circularly polarized spectra for the first time. Linear polarization position angles and circular polarization Zeeman splitting observed in the maser emission permit interpretation of a comprehensive picture of the magnetic field at the supernova/molecular cloud interface marked by the masers. We find the post-SNR shock magnetic field to be well ordered over the ~1 pc covered by the maser region (compared with the approximately 30 pc diameter of the entire SNR) and well aligned with the shock front that is traced by synchrotron radiation and molecular emission. Based on MERLIN data having a resolution of 200 mas and VLBA data with a resolution of 15 mas, the masers are measured to have deconvolved angular sizes of 90-350 mas (225-875 AU) with compact cores 20 mas (50 AU) in size, consistent with theoretical expectation and previous observations.
Modeling the growth of Listeria monocytogenes on the surface of smear- or mold-ripened cheese

Surface-ripened cheeses are matured by means of manual or mechanical technologies posing a risk of cross-contamination, if any cheeses are contaminated with Listeria monocytogenes. In predictive microbiology, primary models are used to describe microbial responses, such as growth rate over time and secondary models explain how those responses change with environmental factors. In this way, primary models were used to assess the growth rate of L. monocytogenes during ripening of the cheeses and the secondary models to test how much the growth rate was affected by either the pH and/or the water activity (aw) of the cheeses. The two models combined can be used to predict outcomes. The purpose of these experiments was to test three primary (the modified Gompertz equation, the Baranyi and Roberts model, and the Logistic model) and three secondary (the Cardinal model, the Ratowski model, and the Presser model) mathematical models in order to define which combination of models would best predict the growth of L. monocytogenes on the surface of artificially contaminated surface-ripened cheeses. Growth on the surface of the cheese was assessed and modeled. The primary models were firstly fitted to the data and the effects of pH and aw on the growth rate (μmax) were incorporated and assessed one by one with the secondary models. The Logistic primary model by itself did not show a better fit of the data among the other primary models tested, but the inclusion of the Cardinal secondary model improved the final fit. The aw was not related to the growth of Listeria. This study suggests that surface-ripened cheese should be separately regulated within EU microbiological food legislation and results expressed as counts per surface area rather than per gram.
The Intrinsic Constraint Model for Stereo-Motion Integration

How the visual system integrates the information provided by several depth cues is central for vision research. Here, we present a model for how the human visual system combines disparity and velocity information. The model provides a depth interpretation to a subspace defined by the covariation of the two signals. We show that human performance is consistent with the predictions of the model, and compare them with those of another theoretical approach, the modified weak-fusion model. We discuss the validity of each approach as a model for human perception of 3-D shape from multiple cues to depth.
Blood Pressure Variability and Its Management in Hypertensive Patients

Optimizing treatment for hypertension has focused on reducing cardiovascular risk through reduction of mean blood pressure (BP) under the basic assumption that lower is better, as long as diastolic BP is sufficient to maintain coronary perfusion. However, antihypertensive therapy as currently practiced does not eliminate all hazards associated with BP elevation. Blood pressure variability (BPV) correlates closely with target-organ damage independent of mean BP and transient increases in BP are also triggers of vascular events. So far, there is no definitive outcome data relating specific reduction in BPV to decline cardiovascular events or death. Thus, the decision whether BPV should be considered a new therapeutic target is left to the clinical judgment of physicians and individualized for each patient. However, new evidence suggests that taking an antihypertensive medication at bedtime significantly affects BPV and lowers the risk of cardiovascular events and death. This strategy may provide a means of individualizing treatment of hypertension according to the circadian BPV of each patient and may be a new option to optimize BP control and reduce risk.
Anticipatory quality adaptation for mobile streaming: Fluent video by channel prediction

This demonstration shows a new type of HTTP adaptive streaming (HAS) for mobile users. We will present an anticipatory HAS policy that adapts video quality based on a prediction of the wireless channel state. By anticipating a poor channel state and by reducing video quality in advance, this policy maximizes the number of seconds in the user's playout buffer before coverage is lost. Even in difficult coverage situations such as tunnels and elevators, our approach reaches outstanding fluency without decreasing the average video bitrate. With this anticipatory buffering technique users require no channel resources at low channel state, which increases spectral efficiency. Our solution is based on an modified player application and will be demonstrated on off-the-shelf Smartphones in a conventional 4G network.
Endoplasmic reticulum–endosome contact increases as endosomes traffic and mature

Endosomes do not traffic autonomously but instead associate with the ER membrane. ER tubules wrap around and maintain contact with both early and late endosomes by ER ring rearrangements. As endosomes mature, they increase the degree of their ER association, which suggests that the ER might play a role in endosomal maturation.
Leveraging a critical care database: selective serotonin reuptake inhibitor use prior to ICU admission is associated with increased hospital mortality.

BACKGROUND Observational studies have found an increased risk of adverse effects such as hemorrhage, stroke, and increased mortality in patients taking selective serotonin reuptake inhibitors (SSRIs). The impact of prior use of these medications on outcomes in critically ill patients has not been previously examined. We performed a retrospective study to determine if preadmission use of SSRIs or serotonin norepinephrine reuptake inhibitors (SNRIs) is associated with mortality differences in patients admitted to the ICU. METHODS The retrospective study used a modifiable data mining technique applied to the publicly available Multiparameter Intelligent Monitoring in Intensive Care (MIMIC) 2.6 database. A total of 14,709 patient records, consisting of 2,471 in the SSRI/SNRI group and 12,238 control subjects, were analyzed. The study outcome was in-hospital mortality. RESULTS After adjustment for age, Simplified Acute Physiology Score, vasopressor use, ventilator use, and combined Elixhauser score, SSRI/SNRI use was associated with significantly increased in-hospital mortality (OR, 1.19; 95% CI, 1.02-1.40; P=.026). Among patient subgroups, risk was highest in patients with acute coronary syndrome (OR, 1.95; 95% CI, 1.21-3.13; P=.006) and patients admitted to the cardiac surgery recovery unit (OR, 1.51; 95% CI, 1.11-2.04; P=.008). Mortality appeared to vary by specific SSRI, with higher mortalities associated with higher levels of serotonin inhibition. CONCLUSIONS We found significant increases in hospital stay mortality among those patients in the ICU taking SSRI/SNRIs prior to admission as compared with control subjects. Mortality was higher in patients receiving SSRI/SNRI agents that produce greater degrees of serotonin reuptake inhibition. The study serves to demonstrate the potential for the future application of advanced data examination techniques upon detailed (and growing) clinical databases being made available by the digitization of medicine.
Effect of srtA and srtB gene expression on the virulence of Staphylococcus aureus in animal models of infection.

OBJECTIVE The role that the surface proteins anchored by the srtA and srtB gene products play in the ability of Staphylococcus aureus bacteria to establish infection was investigated in several animal models. METHODS Wild-type and corresponding mutants with deletions of the srtA and/or srtB genes were used in murine acute lethal infection, septic arthritis, kidney infection and rat endocarditis models. RESULTS The LD(50) of the wild-type and srtB- knockout were comparable and approximately two- to four-fold lower than the required inoculum of the srtA- and srtA-B- strains. This difference was exhibited as a two-fold greater mortality at the highest inoculum. The wild-type strain established arthritic inflammation in over 90% of the animals with a maximum arthritic index of 6.5 by days 17-21. The srtB- knockout was able to cause inflammation in 70-80% of the mice, but with a lower index of 3.0. Both the srtA- and srtA-B- strains appeared to be less virulent in this model with arthritic indices of around 0.5 and only 20% of the animals with inflammation. Strains with the srtA mutation achieved statistically significant lower titres than wild-type in kidneys of mice after intravenous infection. Mean bacterial counts in cardiac vegetations were significantly higher for the wild-type and srtB- strain compared with the srtA- and srtA-B- strains. CONCLUSION Results from this study substantiate the role of the srtA gene product in the establishment of infections and further studies are warranted to define and exploit this as a target for antimicrobial chemotherapy.
Assessing the Chaotic Nature of Neural Networks

During the course of brain development there exists a brief period of exuberant synaptic formation followed by an equally impressive pruning and strengthening of surviving synapses that eventually form the basis of the adult brain. The root factor in shaping this process is the information we receive from the world in this critical period of development, the effects of which last a life-time. As we learn neural circuits are fine tuned to accomplish meaningful tasks be they locomotion, communication or any other of the myriad of cognitive facilities we possess. In the process uncertainty gives way to programmatic perfection, those shaky first steps become effortless strides. With this in mind I hypothesized that learning reduces chaos in neural circuits. Below is an initial proof of concept for accessing the chaotic nature of neural circuits.
Biases in abundance derivations for metal-rich nebulae

Using ab-initio photoionization models of giant H ii regions, we test methods for abundance determinations based on a direct measurement of the electron temperature, now possible even for moderate to high-metallicity objects. We find that, for metallicities larger than solar, the computed abundances deviate systematically from the real ones, generally by larger amounts for more metal-rich H ii regions. We discuss the reasons for this, and present diagrams allowing the reader to better understand the various factors coming into play. We briefly discuss less classical methods to derive abundances in metal-rich H ii regions. In particular, we comment on the interest of the oxygen and carbon recombination lines. We also show that, contrary to the case of giant H ii regions, the physical conditions in bright extragalactic planetary nebulae are such that their chemical composition can be accurately derived even at high metallicities. Thus, extragalactic planetary nebulae are promising potential probes of the metallicity of the interstellar medium in the internal parts of spiral galaxies as well as in metal-rich elliptical galaxies.
Bacteremia in patients with hematological malignancies. Analysis of risk factors, etiological agents and prognostic indicators.

BACKGROUND AND OBJECTIVE Patients with hematological malignancies are at increased risk for developing bacteremia. No previous study has investigated the risk and prognostic indicators of bacteremia in such patients using a statistical approach. METHODS A case-control study was performed in 106 patients with hematological malignancies (group A). Two hundred and twelve patients were included as controls and divided into two groups: 106 patients with hematological malignancy without bacteremia (group B) and 106 HIV-infected patients with bacteremia (group C). RESULTS At univariate analysis, bacteremia risk factors in group A were: neutropenia for more than six days (p = 0.03 vs. group B), central venous catheter usage (p = 0.04) and absence of antibiotic prophylaxis (p = 0.03). At multivariate analysis, the use of CVC and neutropenia were independent bacteremia risk factors. The most frequent etiological agents were: Staphylococcus epidermidis and Pseudomonas aeruginosa. Comparing groups A and C, the distribution of Staphylococcus spp. was different, with S. epidermidis being prevalent in hematological patients only. As regards gram-negative organisms, it is of note that no episode of NT-Salmonella bacteremia was observed in group A, unlike group C, where they represent the second leading etiological agents. In group A, 14% of the patients died. Persistent neutropenia (p = 0.01) and the presence of relapsed neoplasm (p = 0.04) were prognostic indicators of bacteremia. INTERPRETATION AND CONCLUSIONS Our findings suggest that bacteremia in patients with hematological malignancies strictly correlates with the intensity and length of neutropenia and CVC usage. Although we observed a low mortality rate, we stress that this clinical condition requires special attention from the physician, who must recognize and treat it promptly.
Multiclass Flow Line Models of Semiconductor Manufacturing Equipment for Fab-Level Simulation

For multiclass flow line models, we identify a class of service times that allow a decomposition of the system into subsets of servers called channels. In each channel, the customer delay is well structured and we develop a recursion to calculate it. The recursions provide an alternative to the elementary evolution equations. By considering batch arrivals and restricting the structure of the model, the recursions can require nearly one order of magnitude less computation than is otherwise possible. Flow lines can be used as models for semiconductor manufacturing equipment such as multicluster or clustered photolithography tools. The models allow for internal wafer buffers and setups that are wafer location dependent. The models have shown to be very accurate in tests with data from clustered photolithography tools in production. As such, the models may serve as good candidates to improve the fidelity of existing equipment models in fab level simulation.
High resolution soft x-ray spectroscopy of the elliptical galaxy NGC 5044. Results from the reflection grating spectrometer on-board XMM-Newton

The results from an X-ray spectroscopic study of the giant elliptical galaxy NGC 5044 in the center of a galaxy group are presented. The line dominated soft X-ray spectra (mainly Fe-L and $\ion{O}{viii}$ ${\rm Ly\alpha}$) from the diffuse gas are resolved for the first time in this system with the Reflection Grating Spectrometers on-board XMM-Newton and provide a strong constraint on the temperature structure. The spectra integrated over 2´ (~20 kpc) in full-width can be described by a two temperature plasma model of 0.7 keV and 1.1 keV. Most of the latter component is consistent with originating from off-center regions. Compared to the isobaric cooling flow prediction, the observation shows a clear cut-off below a temperature of $0.6\pm0.1$ keV. Furthermore, the Fe and O abundances within the central 10–20 kpc in radius are accurately measured to be $0.55\pm0.05$ and $0.25\pm0.1$ times the solar ratios, respectively. The observed cut-off temperature of this galaxy and other central galaxies in galaxy groups and clusters are compared with the scale of the galaxy and properties of the surrounding intra-cluster medium. Based on this comparison, the origin of the lack of predicted cool emission is discussed.