Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembly, heterogeneity, and breaching of the basement membranes

Basement membranes are thin sheets of self-assembled extracellular matrices that are essential for embryonic development and for the homeostasis of adult tissues. They play a role in structuring, protecting, polarizing, and compartmentalizing cells, as well as in supplying them with growth factors. All basement membranes are built from laminin and collagen IV networks stabilized by nidogen/perlecan bridges. The precise composition of basement membranes, however, varies between different tissues. Even though basement membranes represent physical barriers that delimit different tissues, they are breached in many physiological or pathological processes, including development, the immune response, and tumor invasion. Here, we provide a brief overview of the molecular composition of basement membranes and the process of their assembly. We will then illustrate the heterogeneity of basement membranes using two examples, the epithelial basement membrane in the gut and the vascular basement membrane. Finally, we examine the different strategies cells use to breach the basement membrane.
SCG3 Transcript in Peripheral Blood Is a Prognostic Biomarker for REST-Deficient Small Cell Lung Cancer

Purpose: Specific markers of circulating tumor cells may be informative in managing lung cancer. Because the RE-1 silencing transcription factor (REST/NRSF) is a transcriptional repressor that is inactivated in neuroendocrine lung cancer, we identified REST-regulated transcripts (CHGA, CHGB, SCG3, VGF, and PCSK1) for evaluation as biomarkers in peripheral blood. Experimental Design: Transcripts were screened across lung cancer and normal cell lines. Candidates were assessed by reverse transcription-PCR and hybridization of RNA extracted from the peripheral blood of 111 lung cancer patients obtained at clinical presentation and from 27 cancer-free individuals. Results: Expression profiling revealed multiple chromogranin transcripts were readily induced on REST depletion, most notably SCG3 was induced >500-fold. The SCG3 transcript was also overexpressed by 12,000-fold in neuroendocrine compared with nonneuroendocrine lung cancer cells. In peripheral blood of lung cancer patients and cancer-free individuals, we found that SCG3 was more tumor-specific and more sensitive than other chromogranin transcripts as a biomarker of circulating tumor cells. Overall, 36% of small cell lung cancer (SCLC) and 16% of non-SCLC patients scored positively for normalized SCG3 transcript. This correlated with worse survival among SCLC patients with limited disease (n = 33; P = 0.022) but not extensive disease (n = 29; P = 0.459). Interestingly, the subcohort of 6 SCLC patients with resistance to platinum/etoposide chemotherapy all scored positively for peripheral blood SCG3 transcript (P = 0.022). Conclusions: SCG3 mRNA, a component of the REST-dependent neurosecretory transcriptional profile, provides a sensitive prognostic biomarker for noninvasive monitoring of neuroendocrine lung cancer.
Considerações Paleoambientais do Holoceno Médio por Meio de Fitólitos na Serra do Cadeado, Paraná

This study analyzed a sedimentary core of 130 cm depth containing about 30 cm of peaty bulk at its top, obtained from an unnamed pond located at Morro da Pedra Branca, in the municipality of Ortigueira, Parana. The phytoliths present in the peaty sediment were identified and quantified. Three transects on three different microscopy slides were analyzed using an optical microscope with 40x zoom in each sample, totaling 13 samples. At 30 cm depth, the sedimentary bulk was dated at 5,372 years cal. BP using 14C. The following phytolith indexes were calculated: Tree Cover Density, Water Stress and Humidity. The results enabled us to conclude that the pond had a slow sedimentation rate (~ 1 cm/179 years). The most frequent morphotypes were from the Poaceae family (Rondel, Saddle, Bilobate), inferring predominantly grassland vegetation, with absence of the Arecaceae family (palm trees), a high producer of phytoliths of the Globular echinate morphotype. The phytolith assemblages found in the area indicate drier conditions in the Middle Holocene, moving toward to more humid climate conditions today. The interpretations corroborate other paleoenvironmental studies already carried out in the states of Parana and Mato Grosso do Sul, where the existence of a drier period in the Middle Holocene has been demonstrated.
Validity and reliability of exposure assessors' ratings of exposure intensity by type of occupational questionnaire and type of rater.

BACKGROUND In epidemiologic studies that rely on professional judgment to assess occupational exposures, the raters' accurate assessment is vital to detect associations. We examined the influence of the type of questionnaire, type of industry, and type of rater on the raters' ability to reliably and validly assess within-industry differences in exposure. Our aim was to identify areas where improvements in exposure assessment may be possible. METHODS Subjects from three foundries (n = 72) and three textile plants (n = 74) in Shanghai, China, completed an occupational history (OH) and an industry-specific questionnaire (IQ). Six total dust measurements were collected per subject and were used to calculate a subject-specific measurement mean, which was used as the gold standard. Six raters independently ranked the intensity of each subject's current job on an ordinal scale (1-4) based on the OH alone and on the OH and IQ together. Aggregate ratings were calculated for the group, for industrial hygienists, and for occupational physicians. We calculated intra-class correlation coefficients (ICCs) to evaluate the reliability of the raters. We calculated the correlation between the subject-specific measurement means and the ratings to evaluate the raters' validity. Analyses were stratified by industry, type of questionnaire, and type of rater. We also examined the agreement between the ratings by exposure category, where the subject-specific measurement means were categorized into two and four categories. RESULTS The reliability and validity measures were higher for the aggregate ratings than for the ratings from the individual raters. The group's performance was maximized with three raters. Both the reliability and validity measures were higher for the foundry industry than for the textile industry. The ICCs were consistently lower in the OH/IQ round than in the OH round in both industries. In contrast, the correlations with the measurement means were higher in the OH/IQ round than in the OH round for the foundry industry (group rating, OH/IQ: Spearman rho = 0.77; OH: rho = 0.64). No pattern by questionnaire type was observed for the textile industry (group rating, Spearman rho = 0.50, both assessment rounds). For both industries, the agreement by exposure category was higher when the task was reduced to discriminating between two versus four exposure categories. CONCLUSIONS Assessments based on professional judgment may reduce misclassification by using two or three raters, by using questionnaires that systematically collect task information, and by defining intensity categories that are distinguishable by the raters. However, few studies have the resources to use multiple raters and these additional efforts may not be adequate for obtaining valid subjective ratings. Thus, improving exposure assessment approaches for studies that rely on professional judgment remain an important research need.
Coding vs. Packet Retransmission over Noisy Channels

In many packet-based communication systems such as TCP/IP-based systems, packets are communicated over a noisy physical layer (a channel), and if a packet cannot be decoded correctly, then the transport layer retransmits it. Of course, retransmissions consume significant resources and their use should be limited. However, decreasing the likelihood of retransmission requires to encode the packets with strong channel codes in the physical layer, which also requires additional channel resources. In this paper, we study the cross-layer tradeoff between coding and packet retransmissions, and optimize over the total channel resource consumption. We show that as the packet length k increases, the redundancy r beyond the k/C channel uses implied by Shannon's channel capacity C is Theta(radickln(k)) extra channel uses. Moreover, as k increases we must use stronger channel codes. We then apply these results to universal coding over a piecewise memoryless channel with transitions between unknown i.i. d. statistics. Our constructive universal algorithm has redundancy r=O(k2/3radicln(k)) using packets of polynomially increasing lengths while accounting for possible packet drops caused by transitions in the statistics.
A Random Walk in the Park: An Individual-Based Null Model for Behavioral Thermoregulation

Behavioral thermoregulators leverage environmental temperature to control their body temperature. Habitat thermal quality therefore dictates the difficulty and necessity of precise thermoregulation, and the quality of behavioral thermoregulation in turn impacts organism fitness via the thermal dependence of performance. Comparing the body temperature of a thermoregulator with a null (non-thermoregulating) model allows us to estimate habitat thermal quality and the effect of behavioral thermoregulation on body temperature. We define a null model for behavioral thermoregulation that is a random walk in a temporally and spatially explicit thermal landscape. Predicted body temperature is also integrated through time, so recent body temperature history, environmental temperature, and movement influence current body temperature; there is no particular reliance on an organism’s equilibrium temperature. We develop a metric called thermal benefit that equates body temperature to thermally dependent performance as a proxy for fitness. We measure thermal quality of two distinct tropical habitats as a temporally dynamic distribution that is an ergodic property of many random walks, and we compare it with the thermal benefit of real lizards in both habitats. Our simple model focuses on transient body temperature; as such, using it we observe such subtleties as shifts in the thermoregulatory effort and investment of lizards throughout the day, from thermoregulators to thermoconformers.
Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis

Multiple changes at the DNA level are at the basis of complex diseases. Identifying the genetic networks that are influenced by these changes might help in understanding the development of these diseases. Canonical correlation analysis is used to associate gene expressions with DNA-markers and thus reveals sets of co-expressed and co-regulated genes and their associating DNA-markers. However, when the number of variables gets high, e.g. in the case of microarray studies, interpretation of these results can be difficult. By adapting the elastic net to canonical correlation analysis the number of variables reduces, and interpretation becomes easier, moreover, due to the grouping effect of the elastic net co-regulated and co-expressed genes cluster. Additionally, our adaptation works well in situations where the number of variables exceeds by far the number of subjects.
5α‐reductase type 3 expression in human benign and malignant tissues: A comparative analysis during prostate cancer progression

A third isozyme of human 5α‐steroid reductase, 5α‐reductase‐3, was identified in prostate tissue at the mRNA level. However, the levels of 5α‐reductase‐3 protein expression and its cellular localization in human tissues remain unknown.
Antinociceptive and antidiarrheal effects of pioglitazone in a rat model of diarrhoea‐predominant irritable bowel syndrome: Role of nitric oxide

Irritable bowel syndrome (IBS) is a prevalent disease characterized by abdominal pain and abnormal bowel habits. Pioglitazone is a peroxisome proliferator‐activated receptor (PPAR) γ agonist and, although it is mostly used as an antidiabetic agent, it has been reported to have analgesic effects. Nitric oxide (NO), a gaseous molecule that mediates many of the effects of pioglitazone, has been implicated in the pathophysiology of IBS. The aim of the present study was to investigate the effects of pioglitazone on symptoms in a rat model of diarrhoea‐predominant IBS (D‐IBS). and to determine the role of NO in these effects. Diarrhoea‐predominant IBS was induced by intracolonic instillation of acetic acid. Pioglitazone (2 mg/kg, i.p.) was administered on Days 7, 9 and 11 after acetic acid instillation. To investigate the mechanism involved in pioglitazone action, rats were also administered either the PPARγ antagonist GW9662 (3 mg/kg, i.p.), the NO synthase (NOS) inhibitor NG‐nitro‐l‐arginine methyl ester (l‐NAME; 10 mg/kg, i.p.) or the NO precursor l‐arginine (250 mg/kg, i.p.) along with pioglitazone. Visceral hypersensitivity, nociceptive thresholds, defecation frequency, stool form, serum and colon NO production and inducible (i) NOS activity were assessed 1 h after the final injection of pioglitazone or dimethylsulphoxide (used as the vehicle). Pioglitazone reduced visceral hypersensitivity and defecation frequency, increased nociceptive thresholds, NO production and iNOS activity and shifted stool form towards hard stools in D‐IBS rats. These effects of pioglitazone were significantly reversed by l‐NAME, but not GW9662. l‐Arginine augmented the effects of pioglitazone. In conclusion, pioglitazone alleviates symptoms in a rat model of D‐IBS through an NO‐dependent mechanism.
Updated Italian checklist of Soldier Flies (Diptera, Stratiomyidae)

Abstract An updated checklist for Stratiomyidae of Italy is presented. Previous knowledge and information are put together in a comprehensive way, integrated also with results obtained by sampling with Malaise traps in some of the test areas of the LIFE+ project ManFor C.BD. At the time of writing, with 91 known species, the Italian fauna of Stratiomyidae is the richest in Europe. Neopachygaster meromelas (Dufour, 1841) and Zabrachia minutissima (Zetterstedt, 1838) are new to the Italian fauna. A comprehensive key to the European species of Chorisops Rondani, 1856 is given.
Investigation of Acoustic Waves in the Ionosphere Generated by a Deep Convection System Using Distributed Networks of GPS Receivers and Numerical Modeling

Acoustic waves generated in the lower atmosphere may become an important source of variability in the upper atmosphere. Although excited with small amplitudes compared to gravity waves, they are minimally subjected to viscous dissipation and may reach large amplitudes at F region altitudes. We present total electron content data from a dense network of ground‐based GPS receivers during an outbreak of severe weather over Kansas on 26 May 2016. The results show annular traveling ionospheric disturbances (TIDs) propagating radially outward from the center of the storm. The TID characteristics were consistent with acoustic waves in the infrasonic range. We have modeled the disturbance by including a heat source representing latent heat release from a large thunderstorm. The modeled disturbance at ionospheric altitudes resembles the TIDs in terms of phase speed, frequency, and horizontal wavelength. We conclude that the observed TIDs were caused by an acoustic wave generated by deep convection.
Crop Coefficient Based Evapotranspiration Estimates Compared with Mechanistic Model Results

Daily evapotranspiration (ET) estimates from reference ET (ET ) values multiplied R by a crop coefficient (K ) have been the standard method for irrigation scheduling purposes C for many years. However, curves of K vs. cumulative growing degree days (CGDD) or C days after planting are averages of data from several individual years and the K value from C such a curve may vary considerably from the K value for any given year. Mechanistic C models may be more accurate but also require more data about the crop. Typically, a mechanistic model will require information about the leaf area index (LAI) and rooting depth on a daily basis to provide good ET estimates. Both the mechanistic model and the reference ET equations typically require meteorological information such as wind speed, solar radiation, air temperature, and relative humidity. We compared ET estimated using crop coefficients developed at our location for winter wheat (Triticum aestivum L.) with ET estimated by the mechanistic model ENWATBAL and ET measured by weighing lysimeters for three years of winter wheat grown on the southern high plains. Values of LAI were measured periodically in the field and a spline fit interpolation was used to describe the evolution of LAI on a daily basis throughout each year. In addition, a general curve of LAI vs. CGDD was developed from the data from all three years and used to parameterize ENWATBAL. For all years the ENWATBAL model using field measured LAI data gave better estimates of daily and cumulative ET than those derived from K and ET . For two C R of three years the ENWATBAL model using the general LAI vs. CGDD curve predicted ET better than K and ET . However, when five day cumulative ET values were compared C R the K and ET method gave more accurate estimates that ENWATBAL. For multiple day C R forecasting and irrigation scheduling the K and ET method is preferable to ENWATBAL C R but ENWATBAL is more useful if frequent irrigations must be made or if crop coefficients are not available. WATER RESOURCES ENGINEERING 1586
Inhibition of Src family kinases enhances retinoic acid–induced gene expression and myeloid differentiation

Treatment of acute promyelocytic leukemia with retinoic acid (RA) results in differentiation of the leukemic cells and clinical remission. However, the cellular factors that regulate RA-induced myeloid differentiation are largely unknown, and other forms of acute myelogenous leukemia (AML) do not respond to this differentiation therapy. A greater understanding of the molecules that positively or negatively regulate RA-induced differentiation should facilitate the development of more effective differentiation therapies. In this study, we investigated the potential role of Src family kinases (SFK) in the regulation of RA-induced gene expression and myeloid differentiation. We report that inhibition of SFKs markedly enhanced RA-induced differentiation in myeloid cell lines and primary AML cells, as assessed by flow-cytometric analysis of cell surface markers, morphologic analysis, and nitroblue tetrazolium reduction. In addition, inhibition of SFKs enhanced expression from retinoic acid receptor (RAR) target genes encoding CCAAT/enhancer binding protein ε (C/EBPε), PU.1, intercellular adhesion molecule-1 (ICAM-1), and cathepsin D. Moreover, a constitutively active Src inhibited RAR-dependent transcription, whereas a kinase-dead Src exerted little effect. These studies provide the first demonstration that SFKs act to negatively regulate RA-induced gene expression and myeloid differentiation and suggest that the combination of SFK inhibition and RA treatment may be therapeutically beneficial in AML. [Mol Cancer Ther 2007;6(12):3081–90]
Modification of the Trypsin-Dependent Cleavage Activation Site of the Human Metapneumovirus Fusion Protein To Be Trypsin Independent Does Not Increase Replication or Spread in Rodents or Nonhuman Primates

ABSTRACT The contribution of cleavage activation of the fusion F protein of human metapneumovirus (HMPV) to replication and pathogenicity in rodents and nonhuman primates was investigated. Recombinant HMPVs were generated in which the naturally occurring trypsin-dependent cleavage sequence (R-Q-S-R↓) was replaced by each of three sequences whose cleavage in vitro does not depend upon added trypsin. Two of these were multibasic sequences derived from avian metapneumovirus type A (R-R-R-R) or type C (R-K-A-R), with the former containing the consensus furin protease cleavage motif (R-X-R/K-R↓). The third one (R-Q-P-R) was derived from a recently described trypsin independent HMPV isolate (J. H. Schickli, J. Kaur, N. Ulbrandt, R. R. Spaete, and R. S. Tang, J. Virol. 79:10678-10689, 2005). To preclude the possibility of conferring even greater virulence to this significant human pathogen, the modifications were done in an HMPV variant that was attenuated by the deletion of two of the three envelope glycoproteins, SH and G. Each of the introduced cleavage sequences conferred trypsin independent F cleavage and growth to HMPV in vitro. However, they differed in the efficiency of trypsin independent growth and plaque formation in vitro: R-R-R-R > R-K-A-R > R-Q-P-R > R-Q-S-R. The R-R-R-R mutant was the only one whose growth in vitro was not augmented by added trypsin, indicative of highly efficient trypsin independent cleavage. When inoculated intranasally into hamsters, there was essentially no difference in the magnitude of replication in the upper or lower respiratory tract between the mutants, and virus was not detected in organs outside of the respiratory tract. Evaluation of the most cleavage-efficient mutant, R-R-R-R, in African green monkeys showed that there was no detectable change in the magnitude of replication in the upper and lower respiratory tract or in immunogenicity and protective efficacy against HMPV challenge. These results suggest that cleavage activation is not a major determinant of HMPV virulence.
Regression and Ranking based Optimisation for Sentence Level MT Evaluation

Automatic evaluation metrics are fundamentally important for Machine Translation, allowing comparison of systems performance and efficient training. Current evaluation metrics fall into two classes: heuristic approaches, like BLEU, and those using supervised learning trained on human judgement data. While many trained metrics provide a better match against human judgements, this comes at the cost of including lots of features, leading to unwieldy, non-portable and slow metrics. In this paper, we introduce a new trained metric, ROSE, which only uses simple features that are easy portable and quick to compute. In addition, ROSE is sentence-based, as opposed to document-based, allowing it to be used in a wider range of settings. Results show that ROSE performs well on many tasks, such as ranking system and syntactic constituents, with results competitive to BLEU. Moreover, this still holds when ROSE is trained on human judgements of translations into a different language compared with that use in testing.