Miracle-dz/UniFAR-FTUs huggingface dataset:
Response of Campylobacter jejuni to sodium chloride

Studies were done to provide more comprehensive information on the response of Campylobacter jejuni and nalidixic acid-resistant, thermophilic Campylobacter (NARTC) to sodium chloride at 4, 25, and 42 degrees C. Three strains of C. jejuni were studies, and all could grow at 42 degrees C in the presence of 1.5% NaCl, but not 2.0% NaCl. At the same temperature, NARTC could grow in 2.0% NaCl and was substantially more tolerant to 2.5 and 4.5% NaCl than was C. jejuni. Both C. jejuni and NARTC grew poorly in the absence of added NaCl and grew best in the presence of 0.5% NaCl at 42 degrees C. At 25 degrees C, NaCl concentrations of 1.0 to 2.5% were protective to NARTC, but the same concentrations of salt generally enhanced the rate of death of C. jejuni. At 4 degrees C, both C. jejuni and NARTC were sensitive to 1.0% or more NaCl; however, the rate of death at this temperature was substantially less than that which occurred at 25 degrees C. A 3 log10 decrease of cells occurred in 4.5% NaCl after 1.2 to 2.1 days at 25 degrees C, and a similar reduction in cells took approximately 2 weeks at the same salt concentration and 4 degrees C. Although C. jejuni grows best in the presence of 0.5% NaCl, the presence of NaCl at concentrations as low as 1.0% may retard growth or increase rate of death; hence, it is advisable that growth media used for recovering or enumerating this organism contain 0.5% NaCl, but not 1.0% or more NaCl.
How Long Should Parental Leave Be? Attitudes to Gender Equality, Family, and Work as Determinants of Women’s and Men’s Parental Leave in Sweden

A more equal division of parental leave use between parents has been a major political goal in Sweden for a long time, as it is assumed to lead to gender equality in the labor market, as well as in the homes. The assumed correlation between gender equality and shared parental leave has many aspects, but it has been investigated only in part. In this study, we investigate the determinants of men’s and women’s parental leave use with a focus on attitudes toward family, work, and gender equality. We use the Young Adult Panel Study with surveys conducted in 1999, 2003, and 2009. The findings indicate that gender equality orientation matters for parental leave for fathers. Mothers’ parental leave length is primarily influenced by family orientation, whereas fathers’ is influenced by the economic dimension of work.
The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution.

Electron crystallography has the potential to visualise the charge status of atoms. This is due to the significantly different scattering factors of neutral and ionised atoms for electrons in the low-resolution range (typically less than 5 A). In previous work, we observed two different types of densities around acidic residues in the experimental (|Fo|) map of bacteriorhodopsin (bR), a light-driven proton pump. We suggested that these might reflect different states of the acidic residues; namely, the protonated (neutral) and the deprotonated (negatively charged) state. To evaluate the observed charge more quantitatively, we refined the atomic model for bR and eight surrounding lipids using our electron crystallographic data set between 8.0 and 3.0 A resolution, where the charge effect is small. The refined model yielded an R-factor of 23.7% and a free R-factor of 33.0%. To evaluate the effect of charges on the density map, we calculated a difference (|Fo|-|Fc|) map including data of a resolution lower than 8.0 A resolution, where the charge effect is significant. We found strong peaks in the difference map mainly in the backbone region of the transmembrane helices. We interpreted these peaks to come from the polarisation of the polar groups in the main chain of the alpha-helices and we examined this by assuming a partial charge of 0.5 for the peptide carbonyl groups. The resulting R and free R-factors dropped from 0.250 and 0.341 to 0.246 and 0.336, respectively. Furthermore, we also observed some strong peaks around some side-chains, which could be assigned to positively charged atoms. Thus, we could show that Asp36 and Asp102 are likely to interact with cations nearby. In addition, peaks found around the acidic residues Glu74, Glu194 and Glu212 have different features and might represent positive charges on polarised water molecules or hydroxonium ions.
Intellectual property protection for FPGA designs with soft physical hash functions: First experimental results

The use of Soft Physical Hash (SPH) functions has been recently introduced as a flexible and efficient way to detect Intellectual Property (IP) cores in microelectronic systems. Previous works have mainly investigated software IP to validate this approach. In this paper, we extend it towards the practically important case of FPGA designs. Based on experiments, we put forward that SPH functions-based detection is a promising and low-cost solution for preventing anti-counterfeiting, as it does not require any a-priori modification of the design flow. In particular, we illustrate its performances with stand-alone FPGA designs, re-synthetized FPGA designs, and in the context of parasitic IPs running in parallel.
Pig Abattoir Inspection Data: Can It Be Used for Surveillance Purposes?

Statutory recording of carcass lesions at the abattoir may have significant potential as a resource for surveillance of livestock populations. Food Standards Agency (FSA) data in Great Britain are not currently used for surveillance purposes. There are concerns that the sensitivity of detection, combined with other issues, may make the outputs unreliable. In this study we postulate that FSA data could be used for surveillance purposes. To test this we compared FSA data with BPHS (a targeted surveillance system of slaughtered pigs) and laboratory diagnostic scanning surveillance (FarmFile) data, from mid-2008 to mid-2012, for respiratory conditions and tail bite lesions in pigs at population level. We also evaluated the agreement/correlation at batch level between FSA and BPHS inspections in four field trials during 2013. Temporal trends and regional differences at population level were described and compared using logistic regression models. Population temporal analysis showed an increase in respiratory disease in all datasets but with regional differences. For tail bite, the temporal trend and monthly patterns were completely different between the datasets. The field trials were run in three abattoirs and included 322 batches. Pearson’s correlation and Cohen’s kappa tests were used to assess correlation/agreement between inspections systems. It was moderate to strong for high prevalence conditions but slight for low prevalence conditions. We conclude that there is potential to use FSA data as a component of a surveillance system to monitor temporal trends and regional differences of chosen indicators at population level. At producer level and for low prevalence conditions it needs further improvement. Overall a number of issues still need to be addressed in order to provide the pig industry with the confidence to base their decisions on these FSA inspection data. Similar conclusions, at national level, may apply to other livestock sectors but require further evaluation of the inspection and data collection processes.
Accepting Zeno words without stopping time Research Report LSV

Timed models were introduced to describe the behaviors of real-time systems and, up to now, they were usually required to produce only executions with divergent sequences of times. However, some physical phenomena, as the movements of a damped oscillator, can be represented by convergent executions, producing Zeno words in a natural way. Moreover, time can progress if such an execution can be followed by other ones. We extend the deenition of timed automata, allowing to generate sequences of innnite convergent executions, while keeping good properties for the veriication of systems: emptiness is still decidable. We introduce a new notion of reenement for timed systems, in which actions are replaced by recognizable Zeno languages and we prove that the corresponding class of languages is the closure of the usual one under reenement.
An Improved Set Invariance Analysis and Gain-Scheduled Control of LPV Systems Subject to Actuator Saturation

This paper studies the problem of set invariance analysis and gain-scheduled control for linear parameter-varying systems with actuator saturation. Based on a descriptor model transformation of the system, a less conservative condition is derived by relaxing the stability conditions presented in a previous paper. A linear matrix inequality-based optimization procedure is proposed to obtain the optimal time-invariant state feedback controller. In order to further improve the closed-loop performance, a gain-scheduled controller is constructed by collecting the interactions among the subsystems in a single matrix. Two examples are provided to illustrate the effectiveness of the results.
MDRD Versus CKD-EPI Equation to Estimate Glomerular Filtration Rate in Kidney Transplant Recipients

Background The new Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) creatinine-based equation was developed to address the systematic underestimation of the glomerular filtration rate (GFR) by the Modification of Diet in Renal Disease (MDRD) Study equation in patients with a relatively well-preserved kidney function. The performance of the new equation for kidney transplant recipients is discussed. Methods We analyzed the performances of the CKD-EPI equation in comparison with the MDRD Study equation in 825 stable kidney transplant recipients. Bias, precision, and accuracy within 30% of true GFR were determined. GFR was measured by urinary clearance of inulin (n=488) and plasma clearance of 51Cr-EDTA (n=337). Results Mean measured GFR (mGFR) was 50±19 mL/min/1.73 m2. On the whole cohort, bias was significantly lower for MDRD Study equation compared with CKD-EPI creatinine. This superiority translates into a better accuracy (80% and 74% for the MDRD and CKD-EPI creatinine, respectively). The best performance of the MDRD Study equation is confirmed both in the subgroups of patients with mGFR <60 mL/min/1.73 m2 and between 60 and 90 mL/min/1.73 m2. For mGFR >90 mL/min/1.73 m2, there were no significant differences between the two equations in terms of performance. Conclusions The CKD-EPI creatinine equation does not offer a better GFR prediction in renal transplant patients compared with the MDRD Study equation, even in the earlier CKD stages.
Examining executive function in individuals with brain injury: A review

Background: Patients with aphasia resulting from a stroke may exhibit cognitive impairments in addition to their language disturbance. The ability to detect and quantify executive function impairment, in particular, may be critical to treating these patients. Furthermore, the effects of executive dysfunction on daily activities may interact with or amplify limitations due to their language disorder. Multiple measures exist in the clinical and research neuropsychological literatures for assessing executive function, however these vary in reliability, validity, and language demands. Aims: This review explores the definition of executive function, describes tests of executive function, and makes recommendations regarding their use in populations with language impairment. Initially a literature search was undertaken for reviews and empirical studies addressing the definition and measurement of executive function, as well as studies of cognitive function in patients with frontal lobe damage. Included in this review are tasks on which patients with frontal lesions showed impairments, activations were seen in neuroimaging studies, or which were developed for the purpose of tapping a cognitive process hypothesized to be an executive function. Main Contribution: Studies of cognitive ability in those with aphasia are reviewed. Purported executive function tests are organized into a proposed substructure for grouping executive processes, and are evaluated for their usefulness in assessing those with aphasia. Tests that have been used hint at impairments in some individuals with aphasia, suggesting a need to look at correlation with severity of auditory comprehension and constructional praxis. Conclusions: Although few executive function tests are currently appropriate for use in a language-disordered population without modifications, many have potential. In order to advance our understanding of the construct of executive function, it is important to develop a clearer definition of the processes involved. In the meantime, the tests reviewed here may be helpful in assessing whether cognitive impairment exists in addition to the language dysfunction in those with aphasia.
A New Molecular Predictor of Distant Recurrence in ER-Positive, HER2-Negative Breast Cancer Adds Independent Information to Conventional Clinical Risk Factors

Purpose: According to current guidelines, molecular tests predicting the outcome of breast cancer patients can be used to assist in making treatment decisions after consideration of conventional markers. We developed and validated a gene expression signature predicting the likelihood of distant recurrence in patients with estrogen receptor (ER)–positive, HER2-negative breast cancer treated with adjuvant endocrine therapy. Experimental Design: RNA levels assessed by quantitative reverse transcriptase PCR in formalin-fixed, paraffin-embedded tumor tissue were used to calculate a risk score (Endopredict, EP) consisting of eight cancer-related and three reference genes. EP was combined with nodal status and tumor size into a comprehensive risk score, EPclin. Both prespecified risk scores including cutoff values to determine a risk group for each patient (low and high) were validated independently in patients from two large randomized phase III trials [Austrian Breast and Colorectal Cancer Study Group (ABCSG)-6: n = 378, ABCSG-8: n = 1,324]. Results: In both validation cohorts, continuous EP was an independent predictor of distant recurrence in multivariate analysis (ABCSG-6: P = 0.010, ABCSG-8: P < 0.001). Combining Adjuvant! Online, quantitative ER, Ki67, and treatment with EP yielded a prognostic power significantly superior to the clinicopathologic factors alone [c-indices: 0.764 vs. 0.750, P = 0.024 (ABCSG-6) and 0.726 vs. 0.701, P = 0.003 (ABCSG-8)]. EPclin had c-indices of 0.788 and 0.732 and resulted in 10-year distant recurrence rates of 4% and 4% in EPclin low-risk and 28% and 22% in EPclin high-risk patients in ABCSG-6 (P < 0.001) and ABCSG-8 (P < 0.001), respectively. Conclusions: The multigene EP risk score provided additional prognostic information to the risk of distant recurrence of breast cancer patients, independent from clinicopathologic parameters. The EPclin score outperformed all conventional clinicopathologic risk factors. Clin Cancer Res; 17(18); 6012–20. ©2011 AACR.
The Effect of Anxiety Sensitivity on the Autonomic Nervous Reaction during the Cold Pressor Test: A Pilot Study

This study examined the physiologic response to the cold pressor test (CPT). There are inconsistencies in heart rate variability reaction to the CPT. Spectral analysis is widely used to measure heart rate variability. However, the high-frequency (0.16–0.40 Hz) component, which is an index of parasympathetic nervous system activity, is contaminated by respiratory sinus arrhythmia. Thus, inconsistencies between previous studies may be the result of spectral analysis. Lorenz plot analysis has recently been proposed as a way to quantify the R-R heartbeat interval. The relationship between anxiety sensitivity (AS) and autonomic nervous responses is also unclear. Moreover, subjective pain induced by the CPT is affected by AS. The aims of this study were: (1) to clarify the differences between spectral analysis and Lorenz plot analysis in the CPT, and (2) to determine the influence of AS on the autonomic nervous response. Twenty-four university students participated in this CPT study and were divided into low-AS (n = 9) and high-AS (n = 15) groups, based on Anxiety Sensitivity Index scores. The study included three phases: Rest, CPT, and Recovery. We measured subjective pain and fear of pain as indices of sensation and psychological factors. Autonomic nervous response data were also collected during each phase. Scores for subjective pain did not differ significantly between groups. Scores for fear of pain were higher in the high-AS group, relative to the low-AS group. Our result indicated that spectral analysis did not detect the changes in autonomic nervous responses resulting from the CPT. By contrast, Lorenz plot analysis revealed that a parasympathetic nervous response (CVI) was evoked during the CPT and Recovery phases in the low AS group. According to our results, Lorenz plot analysis is appropriate for investigating the autonomic nervous response during the CPT.
Numerical Prediction and Dynamic Meteorology, 2nd Edn. By G. J. HALTINER and R. T. WILLIAMS. Wiley, 1980. 477 pp. £26.90.

This book is best described as a textbook of modern numerical weather-prediction models. The title places numerical prediction before dynamic meteorology, and this is a fair reflection of the book's emphasis. The structure of the text very much follows the organization of prediction models, and its strengths and weaknesses as a book on dynamic meteorology reflect the current state of the art in modelling. Most of the book is concerned with describing techniques as used now, rather than the historical development that led to the present design of models. It is thus a very useful reference for workers coming into the subject who have to work with an established model, but less useful for those who wish to relate the model design to new developments in dynamical theory. Since, however, there are other books on dynamical meteorology available, but no comparable easily available textbook that describes models, the authors have clearly chosen to give priority to filling an obvious gap. The authors are both based a t the Naval Postgraduate School in Monterey, California, and most of their examples are taken from models developed in the USA; in particular that a t UCLA. This may give the impression that model-development work is more concentrated in the USA than is in fact the case. However, this is perhaps a criticism more appropriate to a review article than a textbook. The authors start by describing the equations of motion in Chapter 1. The treatment is very elementary and most of it would serve as a good introduction to the equations of any branch of fluid dynamics, since the scale analysis that defines the problem to be solved as meteorology is postponed to Chapter 3. Thus the introduction of the hydrostatic assumption in Section 1.6 seems premature, it would have been better treated along with the rest of the scale analysis. This perhaps reflects a bias inevitable in workers concerned with large-scale models where the hydrostatic approximation is usually the only one made. The equations of motion for a hydro-static fluid are regarded as the fundamental ones, and other approximate systems are only used for specialized theoretical studies. However, the use of non-hydrostatic models to describe small-scale weather systems is increasing, and a book with this title should not restrict its scope to models describing only large scales. Chapter 1 continues with a derivation of the equations in spherical coordinates and on various …
Digital focusing of OCT images based on scalar diffraction theory and information entropy

This paper describes a digital method that is capable of automatically focusing optical coherence tomography (OCT) en face images without prior knowledge of the point spread function of the imaging system. The method utilizes a scalar diffraction model to simulate wave propagation from out-of-focus scatter to the focal plane, from which the propagation distance between the out-of-focus plane and the focal plane is determined automatically via an image-definition-evaluation criterion based on information entropy theory. By use of the proposed approach, we demonstrate that the lateral resolution close to that at the focal plane can be recovered from the imaging planes outside the depth of field region with minimal loss of resolution. Fresh onion tissues and mouse fat tissues are used in the experiments to show the performance of the proposed method.
Epstein-Barr Virus Sequence Variation—Biology and Disease

Some key questions in Epstein-Barr virus (EBV) biology center on whether naturally occurring sequence differences in the virus affect infection or EBV associated diseases. Understanding the pattern of EBV sequence variation is also important for possible development of EBV vaccines. At present EBV isolates worldwide can be grouped into Type 1 and Type 2, a classification based on the EBNA2 gene sequence. Type 1 EBV is the most prevalent worldwide but Type 2 is common in parts of Africa. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than Type 2 EBV. Molecular mechanisms that may account for this difference in cell transformation are now becoming clearer. Advances in sequencing technology will greatly increase the amount of whole EBV genome data for EBV isolated from different parts of the world. Study of regional variation of EBV strains independent of the Type 1/Type 2 classification and systematic investigation of the relationship between viral strains, infection and disease will become possible. The recent discovery that specific mutation of the EBV EBNA3B gene may be linked to development of diffuse large B cell lymphoma illustrates the importance that mutations in the virus genome may have in infection and human disease.