Miracle-dz/UniFAR-FTUs huggingface dataset:
The primase of broad-host-range plasmid R1162 is active in conjugal transfer

The broad-host-range plasmid R1162 is conjugally mobilized at high frequency by the IncP-1 plasmid R751 but is poorly mobilized by pOX38, a derivative of the F factor. In both cases, the origin of transfer (oriT) and the Mob proteins of R1162 are required, indicating that these plasmids are mobilized by similar mechanisms. R1162 encodes a primase, essential for vegetative replication of the plasmid, that is made both as a separate protein and as the carboxy-terminal domain of MobA, one of the R1162 mobilization proteins (P. Scholz, V. Haring, B. Wittman-Liebold, K. Ashman, M. Bagdasarian, and E. Scherzinger, Gene 75:271-288, 1989). When R751 is the mobilizing vector, the primase is not required for mobilization of plasmids containing cloned mob-oriT R1162 DNA. However, detectable mobilization of such plasmids by pOX38 requires both the primase and its cognate initiation site, oriented for synthesis of the complement to the transferred strand. The long form of the primase is required for optimal transfer: R1162 replicons lacking this form also are not transferred detectably by pOX38 and are less well mobilized by R751. The distance between oriT and the primase initiation site affects the frequency of mobilization, and this effect is polar in the direction of transfer. Our results indicate that the R1162 primase is active in mobilization of R1162 and suggest that the MobA-linked form is an adaptation increasing its effectiveness during transfer.
Determination of Growth Rate and Yield of Nitrifying Bacteria by Measuring Carbon Dioxide Uptake Rate

Nitrifier growth parameters—the maximum growth rate (μ Amax) and yield (Y A)—were estimated by measuring the rate of carbon dioxide uptake and additional rates of oxygen uptake and ammonia (or nitrite) use. Batch tests in a combined titrimetric and offgas analyzer with enriched Nitrobacter and Nitrosomonas cultures and an activated sludge sample were performed. The measured μ Amax values for the Nitrobacter and Nitrosomonas cultures were 0.67 ± 0.03 day −1 and 0.54 ± 0.09 day −1, while the Y A values were 0.072 ± 0.01 g volatile suspended solids (VSS) · g nitrogen (N) −1 and 0.14 ± 0.02 gVSS · gN −1, respectively. For the activated sludge sample, μ Amax was observed to increase with pH (μ Amax = 0.72 · 3.3 (pH‐7.1)) over the range 6.8 to 7.1. All μ Amax and Y A values determined by this method were similar to those previously reported. Compared with other μ Amax and Y A estimation methods, this method allows for unique μ Amax and Y A estimations for given conditions from a single experiment.
Regulatory pathways linking progenitor patterning, cell fates and neurogenesis in the ventral neural tube

The assembly of neural circuits in the vertebrate central nervous system depends on the organized generation of specific neuronal subtypes. Studies over recent years have begun to reveal the principles and elucidate some of the detailed mechanisms that underlie these processes. In general, exposure to different types and concentrations of signals directs neural progenitor populations to generate specific subtypes of neurons. These signals function by regulating the expression of intrinsic determinants, notably transcription factors, which specify the fate of cells as they differentiate into neurons. In this review, we illustrate these concepts by focusing on the generation of neurons in ventral regions of the spinal cord, where detailed knowledge of the mechanisms that regulate cell identity has provided insight into the development of a number of neuronal subtypes, including motor neurons. A greater knowledge of the molecular control of neural development is likely to have practical benefits in understanding the causes and consequences of neurological diseases. Moreover, recent studies have demonstrated how an understanding of normal neural development can be applied to direct differentiation of stem cells in vitro to specific neuronal subtypes. This type of rational manipulation of stem cells may represent the first step in the development of treatments based on therapeutic replacement of diseased or damaged nervous tissue.
Ferroptosis in Liver Disease: Natural Active Compounds and Therapeutic Implications

Ferroptosis is an emerging type of regulated cell death usually accompanied by the accumulation of ferrous ions (Fe2+) and lipid peroxides. As the metabolic hub of the body, the liver is crucial for iron storage and lipid metabolism. The liver seems to be closely related to ferroptosis through iron and lipid metabolism. Liver disease greatly threatens host health, and exploring effective interventions is essential. Mounting studies have demonstrated that ferroptosis is one of the possible pathogenic mechanisms involved in liver disease. Targeting ferroptosis may provide a promising opportunity for treating liver disease. However, drugs targeting ferroptosis are extremely limited. Therefore, it is an urgent need to develop new and safe ferroptosis regulators. Natural active compounds (NAC), especially those derived from traditional Chinese medicine, have recently shown great therapeutic potential in liver disease via modulating ferroptosis-related genes or pathways. Here, we outline the molecular mechanism of ferroptosis and systematically summarize the regulatory function of NAC on ferroptosis in liver disease. Finally, we discuss the application prospects and potential problems concerning NAC as ferroptosis regulators for managing liver disease.
Korekta językowa polskiej adaptacji Kwestionariusza kodów moralnych (MFQ-PL)

Niniejszy artykuł ma na celu korektę szeregu językowych nieścisłości pomiędzy polskojęzyczną i anglojęzyczną wersją 30-itemowego Kwestionariusza kodów moralnych (Moral Foundations Questionnaire, MFQ) i przedstawienie zrewidowanego polskiego tłumaczenia kwestionariusza, które będzie lepiej przystosowane do badań międzykulturowych. Badacze, którzy nie znają języka polskiego i anglojęzycznej wersji MFQ, mogą nie być świadomi różnic między tymi dwoma wersjami językowymi. Różnice te są z kolei istotne, ponieważ MFQ stosuje się do porównywania fundamentów moralnych pomiędzy różnymi kulturami. Precyzja tłumaczenia jest kluczowa w badaniach międzykulturowych, gdyż rozbieżności w znaczeniu mogą prowadzić do wyciągania błędnych wniosków na temat różnic międzykulturowych. W artykule prezentujemy zrewidowaną wersję polskiego tłumaczenia 30-itemowego MFQ. Uważamy, że trafniej oddaje formę i treść anglojęzycznych itemów. Nasze tłumaczenie potencjalnie przyczyni się do bardziej spójnych porównań fundamentów moralnych pomiędzy polskojęzycznymi i innymi próbami.
Production of a Capsular Polysaccharide by a Marine Filamentous Fungus

The spent seawater medium of 4-day-old-cultures of the filamentous marine fungus Leptosphaeria albopunctata had a high viscosity after the fungus was collected by high-speed centrifugation. Microscopic examination of uncentrifuged mycelium suspended in India ink revealed that the viscosity resulted from capsular material. These capsules became disassociated from the mycelium during centrifugation. Precipitation of the medium of centrifuged cultures with 95% ethyl alcohol yielded a highly anthrone-positive polysaccharide material, composed of large amounts of glucose and minute amounts of mannose. Time course studies of the nutritional requirements for capsular polysaccharide production revealed that the capsular material was produced in large amounts, and on a wide variety of sugars, during the period of rapid growth, but was quickly degraded and presumably remetabolized in older cultures. The amount of capsular material produced was enhanced by NaCl concentrations above that of artificial seawater, and KCl could be substituted for NaCl. The salts MgCl2 and CaCl2 were also required for capsule production by L. albopunctata, although growth was obtained in cultures without added amounts of these constituents. The possible role of these salts in the metabolism of the fungus is discussed.
Waveform-agile sensing for tracking

Waveform-agile sensing is fast becoming an important technique for improving sensor performance in applications such as radar, sonar, biomedicine, and communications. The paper provided an overview of research work on waveform-agile target tracking. From both control theoretic and information theoretic perspectives, waveforms can be selected to optimize a tracking performance criterion such as minimizing the tracking MSE or maximizing target information retrieval. The waveforms can be designed directly based on their estimation resolution properties, selected from a class of waveforms with varying parameter values over a feasible sampling grid in the time-frequency plane, or obtained from different waveform libraries.
Hormone factors play a favorable role in female head and neck cancer risk

Due to lower female incidence, estimates of exogenous and endogenous hormonal factors in head and neck cancers (HNCs, comprising cancers of the oral cavity, oropharynx, hypopharynx, and larynx) among women have been inconsistent and unable to account for key HNC risk factors. We pooled data from 11 studies from Europe, North America, and Japan. Analysis included 1572 HNC female cases and 4343 controls. Pooled odds ratios (ORs) estimates and their 95% confidence intervals (CIs) were calculated using multivariate logistic regression models adjusting for tobacco smoking and alcohol drinking. Lower risk was observed in women who used hormone replacement therapy (HRT) (OR = 0.58; 95% CI: 0.34–0.77). Pregnancy (OR = 0.61; 95% CI: 0.42–0.90) and giving birth (OR = 0.59; 95% CI: 0.38–0.90) at <35 years of age were inversely associated with HNCs. An inverse association with HNC was observed with age at start of HRT use (OR = 0.59; 95% CI: 0.39–0.90) for each additional 10 years and with duration of use (OR = 0.87; 95% CI: 0.76–0.99 for every 3 years). Exogenous female hormone use is associated with a nearly twofold risk reduction in female HNCs. The lower female HNC incidence may, in part, be explained by endogenous and exogenous estrogen exposures.
Long-Term Mortality After Preeclampsia

Background: Many believe that preeclampsia is not associated with future morbidity or mortality. We sought to investigate the long-term risk of mortality in women with preeclampsia, focusing on those known to be subsequently normotensive. Study Design: We ascertained deaths during 24–36 years’ follow-up in a cohort of 37,061 women who delivered in Jerusalem in 1964–1976, including 1,070 women with preeclampsia. We used Cox proportional hazard models to estimate the risk of mortality associated with preeclampsia while controlling for the woman's age and education, history of diabetes, heart disease and low birth weight birth, the husband's social class, and the calendar year at the start of follow-up. Results: Compared with women who were not diagnosed with preeclampsia, the relative risk of death after preeclampsia was 2.1 (95% confidence interval = 1.8–2.5). Deaths from cardiovascular disease contributed most strongly to this increase. Among women with preeclampsia who had subsequent births without preeclampsia, the excess risk of mortality became manifest only after 20 years. Conclusions: These findings, together with other recent cohort studies, define preeclampsia as a risk marker for mortality from cardiovascular disease. They suggest that the observation of a normal blood pressure after preeclampsia should not discourage the search for other cardiovascular risk factors or abrogate the need for other preventive measures.
Outgoing Audits of Natural Resource Assets, Environmental Regulation and Environmental Investment in Heavily Polluting Enterprises

: Based on the event of outgoing audits of natural resource assets pilot, this paper selects the data of listed A-share companies from 2011-2018 to empirically test the environmental governance effect of outgoing audits of natural resource assets at the level of heavily polluting enterprises. The study finds that outgoing audits of natural resource assets significantly increase the environmental protection investment of heavily polluting firms in the jurisdiction of pilot cities. It is further found that jurisdictions with stronger environmental regulations weaken the positive effect of outgoing audits of natural resource assets on environmental investments of heavily polluting firms relative to jurisdictions with weaker environmental regulations. The above findings remain robust to parallel trend tests and the inclusion of macro control variables. The findings of the article test the governance effect of outgoing audits of natural resource assets, but the strength of environmental regulation can weaken this effect. This study provides empirical evidence for the environmental governance effect of outgoing audits of natural resource assets.
Within-Subject Variability of Interferon-g Assay Results for Tuberculosis and Boosting Effect of Tuberculin Skin Testing: A Systematic Review

Background Variability in interferon-gamma release assays (IGRAs) results for tuberculosis has implications for interpretation of results close to the cut-point, and for defining thresholds for test conversion and reversion. However, little is known about the within-subject variability (reproducibility) of IGRAs. Several national guidelines recommend a two-step testing procedure (tuberculin skin test [TST] followed by IGRA) for the diagnosis of LTBI. However, the effect of a preceding TST on subsequent IGRA results has been reported in studies with apparently conflicting results. Methodology/Findings We conducted a systematic review to synthesize evidence on within-subject variability of IGRA results and the potential boosting effect of TST. We searched several databases and reviewed citations of previous reviews on IGRAs. We included studies using commercial IGRAs, in addition to non-commercial versions of the ELISPOT assay. Four studies, fulfilling our predefined criteria, examined within-subject variability and 13 studies evaluated TST effects on subsequent IGRA responses. Meta-analysis was not considered appropriate because of heterogeneity in study methods, assays, and populations. Although based on limited data, within-subject variability was present in all studies but the magnitude varied (16-80%) across studies. A TST induced “boosting” of IGRA responses was demonstrated in several studies and although more pronounced in IGRA-positive (i.e. sensitized) individuals, also occurred in a smaller but not insignificant proportion of IGRA-negative subjects. The TST appeared to affect IGRA responses only after 3 days and may apparently persist for several months, but evidence for this is weak. Conclusions/Significance Although reproducibility data are scarce, significant within person IGRA variability has been reported. If confirmed in more studies, this has implications for the interpretation of results close to the cut-point and for definition of conversions and reversions. Although the effect of TST on IGRA results is likely to be inconsequential in IGRA-positive subjects, in IGRA-negative subjects, the interpretation of results may be confounded by a preceding TST if administered more than 3 days prior to an IGRA.
Memory B Cells Are Biased Towards Terminal Differentiation: A Strategy That May Prevent Repertoire Freezing

Isolation of large numbers of surface IgD+CD38− naive and surface IgD−CD38− memory B cells allowed us to study the intrinsic differences between these two populations. Upon in vitro culture with IL-2 and IL-10, human CD40–activated memory B cells undergo terminal differentiation into plasma cells more readily than do naive B cells, as they give rise to five- to eightfold more plasma cells and three- to fourfold more secreted immunoglobulins. By contrast, naive B cells give rise to a larger number of nondifferentiated B blasts. Saturating concentrations of CD40 ligand, which fully inhibit naive B cell differentiation, only partially affect that of memory B cells. The propensity of memory B cells to undergo terminal plasma cell differentiation may explain the extensive extra follicular plasma cell reaction and the limited germinal center reaction observed in vivo after secondary immunizations, which contrast with primary responses in carrier-primed animals. This unique feature of memory B cells may confer two important capacities to the immune system: (a) the rapid generation of a large number of effector cells to efficiently eliminate the pathogens; and (b) the prevention of the overexpansion and chronic accumulation of one particular memory B cell clone that would freeze the available peripheral repertoire.
Molecular characterization of influenza B viruses circulating in northern Italy during the 2001–2002 epidemic season

During the 2001–2002 influenza season, virological surveillance highlighted the predominant circulation of B viruses (86% of isolates) in Italy, in contrast to many other countries in Europe and North America where AH3N2 viruses were isolated most frequently, and in contrast to the infrequent isolation of B viruses in Italy during the previous two years. Associated with this predominance of influenza B was the re‐emergence of B/Victoria/2/87‐lineage viruses, closely related to B viruses prevalent during the 1980s, which are distinct antigenically and genetically from circulating B/Sichuan/379/99‐like viruses of the B/Yamagata/16/88 lineage, which predominated in most parts of the world during the last 10 years. Ninety‐four viruses isolated in two regions of northern Italy were characterized, 50 by direct sequencing of haemagglutinin (HA). Viruses of both Victoria and Yamagata lineages co‐circulated throughout the 12 weeks of the influenza season. The HAs of the Yamagata‐lineage viruses were heterogeneous and comprised two sublineages, represented by B/Sichuan/379/99 and B/Harbin/7/94, whereas the Victoria‐lineage viruses were more homogeneous and closely related to B/Hong Kong/330/01, the current prototype vaccine strain. The antigenic and genetic characteristics of the viruses correlated with certain epidemiological features. In particular, the low age (<14 years) of individuals infected with B/Hong Kong/330/01‐like viruses is likely to reflect the greater susceptibility of the youngest cohort, due to lack of previous exposure to Victoria‐lineage viruses, and is consistent with the conclusion that vaccination with a B/Sichuan/379/99‐like virus would give poor protection against infection with B/Hong Kong/330/01‐like (Victoria‐lineage) viruses. J. Med. Virol. 70:463–469, 2003. © 2003 Wiley‐Liss, Inc.
Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically

Upper thermal limits vary less than lower limits among related species of terrestrial ectotherms. This pattern may reflect weak or uniform selection on upper limits, or alternatively tight evolutionary constraints. We investigated this issue in 94 Drosophila species from diverse climates and reared in a common environment to control for plastic effects that may confound species comparisons. We found substantial variation in upper thermal limits among species, negatively correlated with annual precipitation at the central point of their distribution and also with the interaction between precipitation and maximum temperature, showing that heat resistance is an important determinant of Drosophila species distributions. Species from hot and relatively dry regions had higher resistance, whereas resistance was uncorrelated with temperature in wetter regions. Using a suite of analyses we showed that phylogenetic signal in heat resistance reflects phylogenetic inertia rather than common selection pressures. Current species distributions are therefore more likely to reflect environmental sorting of lineages rather than local adaptation. Similar to previous studies, thermal safety margins were small at low latitudes, with safety margins smallest for species occupying both humid and dry tropical environments. Thus, species from a range of environments are likely to be at risk owing to climate change. Together these findings suggest that this group of insects is unlikely to buffer global change effects through marked evolutionary changes, highlighting the importance of facilitating range shifts for maintaining biodiversity.
Atmospheric Chemistry and Physics Discussions Interactive comment on “ Methane emissions from boreal and tropical forest ecosystems derived from in-situ measurements ”

comment by Peter Bergamaschi, Maarten Krol, Jan Fokke Meirink, and Christian Frankenberg The paper presents two 2-week CH4 measurement time series, one from a boreal measurement site (Hyytiäla , Finland), and one from a tropical forest site (Brownsberg, Surinam). The paper illustrates nicely, how concentration changes in the nocturnal boundary layer can be used to estimate regional sources (or sinks). We want to comment, however, on 3 points:
Deterministic chaos in mobile robots

Autonomous adaptive agents acting in a real or simulated environment exhibit behavioral strategies governed by complex dynamics. In order to have a mathematical description of the behavior of a population of robots, their position is recorded while performing repetitive actions in interaction with the world. The time series is analyzed within the framework of dynamical system theory, using several nonlinear tests to confirm the presence of chaos, including nonlinear prediction error for determinism, cross-prediction error for stationarity and surrogate data testing on time series where nonlinearities have been disrupted. Results show that robots characterized by a chaotic dynamic have a better ability to adapt to known and novel environments. Furthermore, Lyapunov exponent and fractal dimension are correlated with the overall performance of the robots.
Comparison between the ion-specific electrode and SPADNS methods for analysis of fluoride concentration in the water supply

The maintenance of adequate fluoride (F) concentration in the public water supply is fundamental for ensuring that the community use of F can reach the maximum benefit for caries control and minimum risk for dental fluorosis. Thus, surveillance systems must use accurate and valid analytical methods to determine F concentration and, according to the literature, give preference to the ion-specific electrode (F- ISE) analysis. Aim: The objective of this study was to compare the accuracy of the ISE and SPADNS methods in the determination of the F concentration in the same water sample. Methods: Duplicate water samples were taken from 30 sampling sites in the municipality of Maringá, state of Paraná, monthly for 12 months, totaling 276 samples. An aliquot was analyzed by the FOP-UNICAMP Oral Biochemistry laboratory, using the F- ISE method, and the other one, by the SANEPAR laboratory in Maringá/PR, using the SPADNS method. Descriptive analysis and Pearson’s correlation test were applied, with a significant level of p<0.05. Results: Results were expressed as ppm F (mg F/L), and a very strong positive correlation (r= 0.91; p<0.001) was detected between the two methods of analysis. Conclusion: Our findings suggest that the determination of f luoride concentration in water can be made with accuracy by the SPADNS method, a standardized analysis protocol.
Primary Renal Rhabdomyosarcoma: An Unusual Bone Metastasizing Tumor of Kidney

ABSTRACT Rhabdomyosarcoma (RMS) is one of the common malignant tumors in the pediatric age group. There is only a single case report of primary renal alveolar RMS. Fine needle aspiration (FNA) findings of primary renal RMS has not been reported so far. Hence we present an unusual case of primary alveolar RMS of the kidney. An 11 year old boy presented with an abdominal mass. On FNA a diagnosis of undifferentiated sarcoma and anaplastic Wilms tumor were considered. The tumor was resected and showed histopathological features of alveolar rhabdomyosarcoma. He developed multiple bony metastases and succumbed to the illness despite aggressive chemotherapy. RMS of the kidney should be considered in the differential diagnosis of children with a renal mass, and may have an aggressive clinical course with bone metastases.