Miracle-dz/UniFAR-FTUs huggingface dataset:
Life in the ice lane: the winter ecology of stream salmonids

Despite the common view that conditions in winter strongly influence survival and population size of fish, the ecology of salmonids has not been as extensively studied in winter as in other seasons. In this paper, we review the latest studies on salmonid winter survival, habitat use, movement and biotic interactions as they relate to the prevailing physical and habitat conditions in rivers and streams. The majority of research conducted on the winter ecology of salmonids has been carried out in small rivers and streams, where temperatures are above zero and where there is no ice. Investigations in large rivers, regulated and dredged rivers, and under conditions of different ice formations are almost totally lacking, presumably related to sampling difficulties with these systems. The studies‐at‐hand indicate that a multitude of physical and biological factors affect the survival, behavior, and habitat use of salmonids in winter. The general concept that winter functions as a critical period for the survival of young salmonids is not well supported by the literature. Instead, overwinter survival of juvenile fish appears to be context‐dependent, related to specific habitat characteristics and ice regimes of streams. In general, over wintering salmonids prefer sheltered, low velocity microhabitats, are mainly nocturnal, and interact relatively little with conspecifics or interspecifics. Specific descriptions of microhabitat preferences of salmonids are difficult to make due to highly disparate results from the literature. We suggest that future research should be directed towards (1) being able to predict the dynamics of freezing and ice processes at different scales, especially at the local scale, (2) studying fish behavior, habitat use and preference under partial and full ice cover, (3) evaluating the impacts of man‐induced environmental modifications (e. g. flow regulation, land‐use activities) on the ecology of salmonids in winter, and (4) identifying methods to model and assess winter habitat conditions for salmonids. Copyright © 2007 John Wiley & Sons, Ltd.
Risk factors for brain relapse in patients with metastatic breast cancer.

BACKGROUND The occurrence of brain metastases is an emerging problem in patients with metastatic breast cancer. In the present study, we looked at risk factors for brain metastasis among patients with metastatic breast cancer. PATIENTS AND METHODS The risk factors for brain metastasis were first determined in a series of 215 patients with metastatic breast cancer. Risk factors identified in the multivariate analysis were re-evaluated in a confirmatory series of 199 patients with metastatic breast cancer. All the patients had been included in prospective randomized trials that evaluated chemotherapy or endocrine therapy in an adjuvant setting. RESULTS In the first series, the presence of lung metastases (hazard ratio = 4.3, 95% CI: 1.9-9.3, P=0.0003) and negative hormone receptor status (hazard ratio = 4.2, 95% CI: 1.7-11, P=0.002) were the only predictive factors associated with the occurrence of brain metastases in the multivariate analysis. The second series confirmed that the presence of lung metastases and negative hormone receptor status were associated with the occurrence of brain metastases. CONCLUSION The presence of lung metastases as the first site of relapse and a negative hormone receptor status are predictive for the occurrence of brain metastases in patients with metastatic breast cancer. A prophylactic treatment should be evaluated in these subsets of patients.
Are There Differences in the Health Outcomes of Mothers in Europe and East-Asia? A Cross-Cultural Health Survey

The aim of the current study was to investigate differences in quality of life outcomes and depression of mothers in East-Asia and Central Europe. 170 women in Japan and 226 women in Austria with children between 3 and 5 answered the same cross-culturally validated questionnaires. The Quality of Life Questionnaire from the WHO (WHOQOL-Bref), the Patient Health Questionnaire (PHQ-2), the Sense of Coherence Scale (SOC-13), a Social Support Scale (MSPSS), and questions on gender orientation were used. In all dimensions of QOL (physical, psychological, social, and environmental) Japanese women had lower QOL scores compared to Austrian mothers (P < 001). Seven percent of women in both countries experienced major depression. In both countries sense of coherence, experienced stress level, satisfaction with income, social support, and gender roles had an influence on QOL and depressive symptoms. Mothers in Japan consider life events less comprehensible, manageable, and meaningful and experience less support. Consequently, creating an environment where fathers could be more involved in child rearing and mothers have more opportunities to choose between life styles and working and social environments would improve QOL not only in Japanese mothers but also in other countries all over the world.
Pitch period estimation using multipulse model and wavelet transform

Wavelet transform-based pitch period estimation is well known in the literature. This approach to pitch estimation assumes that the glottis closures are correlated with the maxima in the adjacent scales of the wavelet transform and for pitch period estimation, one needs to detect these correlated maxima across these scales, which is often prone to error especially in the case of noisy signals. In this paper, we develop an optimization scheme in the wavelet framework using a multipulse excitation model for the speech signal and the pitch period is estimated as a result of this optimization. We report experiments on both clean and noisy conditions and show that the proposed optimization works better than wide used heuristic approach for maxima detection.
In Vivo Volatile Organic Compound Signatures of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of a chronic enteric disease of ruminants. Available diagnostic tests are complex and slow. In vitro, volatile organic compound (VOC) patterns emitted from MAP cultures mirrored bacterial growth and enabled distinction of different strains. This study was intended to determine VOCs in vivo in the controlled setting of an animal model. VOCs were pre-concentrated from breath and feces of 42 goats (16 controls and 26 MAP-inoculated animals) by means of needle trap microextraction (breath) and solid phase microextraction (feces) and analyzed by gas chromatography/ mass spectrometry. Analyses were performed 18, 29, 33, 41 and 48 weeks after inoculation. MAP-specific antibodies and MAP-specific interferon-γ-response were determined from blood. Identities of all marker-VOCs were confirmed through analysis of pure reference substances. Based on detection limits in the high pptV and linear ranges of two orders of magnitude more than 100 VOCs could be detected in breath and in headspace over feces. Twenty eight substances differed between inoculated and non-inoculated animals. Although patterns of most prominent substances such as furans, oxygenated substances and hydrocarbons changed in the course of infection, differences between inoculated and non-inoculated animals remained detectable at any time for 16 substances in feces and 3 VOCs in breath. Differences of VOC concentrations over feces reflected presence of MAP bacteria. Differences in VOC profiles from breath were linked to the host response in terms of interferon-γ-response. In a perspective in vivo analysis of VOCs may help to overcome limitations of established tests.
The Neurofunctional Mechanisms of Traumatic and Non-Traumatic Memory in Patients with Acute PTSD Following Accident Trauma

Neurofunctional alterations in acute posttraumatic stress disorder (PTSD) and changes thereof during the course of the disease are not well investigated. We used functional magnetic resonance imaging to assess the functional neuroanatomy of emotional memory in surgical patients with acute PTSD. Traumatic (relative to non-traumatic) memories increased neural activity in the amygdala, hippocampus, lateral temporal, retrosplenial, and anterior cingulate cortices. These regions are all implicated in memory and emotion. A comparison of findings with data on chronic PTSD suggests that brain circuits affected by the acute disorder are extended and unstable while chronic disease is characterized by circumscribed and stable neurofunctional abnormalities.
Influence of serological factors and BMI on the blood pressure/hematocrit association in healthy young men and women

The association between mean arterial blood pressure (MAP) and hematocrit (Hct) as a surrogate for blood viscosity was investigated in a young (average 20.0±2.3 years), healthy population of 174 men and 442 women. Health status was assessed by clinical examination and serological evaluation. Individuals with severe anemia or hemoconcentration, prior traumas or major surgical intervention, smokers, and pregnant or lactating women were excluded from the study. The MAP/Hct association was positive and significant (P=0.04) for women and negative, albeit not significantly so, for men. The MAP/Hct association was also evaluated in subgroups of the same population with a progressive step-by-step exclusion of: individuals with cholesterol >200 mg/dL; triglycerides >200 mg/dL; body mass index >25 kg/m2; and glucose >100 mg/dL. This consecutively reduced the strength of the positive MAP/Hct association in women, which became negative – although not significantly so – when all anomalously high factors were excluded. The same trend was found in men. Our study indicates that previously reported positive trends in the relationship between the MAP and Hct in the population are not present in a young, healthy population of men or women that excludes individuals with the confounding factors of above normal serological values and BMI.
Long term health outcomes after injury in working age adults: a systematic review

Background: Estimating the contribution of non-fatal injury outcomes remains a considerable challenge and is one of the most difficult components of burden of disease analysis. The aim of this systematic review was to quantify the effect of being injured compared with not being injured on morbidity and health service use (HSU) in working age adults. Methods: Studies were selected that were population based, had long term health outcomes measured, included a non-injured comparison group, and related to working age adults. Meta-analysis was not attempted because of the heterogeneity between studies. Results: Nine studies met the inclusion criteria. In general, studies found an overall positive association between injury and increased HSU, exceeding that of the general population, which in some studies persisted for up to 50 years after injury. Disease outcome studies after injury were less consistent, with null findings reported. Conclusion: Because of the limited injury types studied and heterogeneity between study outcome measures and follow up, there is insufficient published evidence on which to calculate population estimates of long term morbidity, where injury is a component cause. However, the review does suggest injured people have an increased risk of long term HSU that is not accounted for in current methods of quantifying injury burden.
Endometrial progesterone and estrogen receptors and bleeding disturbances in depot medroxyprogesterone acetate users.

BACKGROUND Depot medroxyprogesterone acetate (DMPA) is a very popular hormonal contraceptive. Unpredictable bleeding disturbances are the main reasons for discontinuation and may be mediated through endometrial hormone receptors. This study was aimed to compare the expression of progesterone and estrogen receptors in the endometrium of bleeding DMPA users with that of amenorrhoeic DMPA users. METHODS Subjects were recruited between April 2000 and January 2001. On the day of the third DMPA injection, 42 amenorrhoeic DMPA users and 42 DMPA users who had frequent or prolonged endometrial bleeding and were bleeding on that day were matched by age and body mass index. Endometrial biopsies were collected for immunohistochemical study of progesterone receptor A plus B (PRAB) and B alone (PRB) and estrogen receptor alpha (ERalpha) and beta (ERbeta) expression. RESULTS There were 23 adequate endometrial samples from each group. There were no differences in any of a series of comparisons of PRAB, PRB, ERalpha and ERbeta expression in glands or stroma between the groups. Serum estradiol and progesterone levels were also not different between the groups. CONCLUSIONS Endometrial PRAB, PRB, ERalpha and ERbeta expression in glands and stroma was not different between DMPA users who had frequent or prolonged bleeding and amenorrhoeic DMPA users.
The Effect of DNA-Dispersed Single-Walled Carbon Nanotubes on the Polymerase Chain Reaction

The unique properties of single-wall carbon nanotubes (SWCNT) make them useful in many new technologies and applications. The interaction of DNA and SWCNT is of interest for many uses, including molecular sensors. This study determined polymerase chain reaction (PCR) efficiency in amplifying a 76 base pair DNA sequence in the presence of SWCNT, of heterogeneous “Mix” and (6,5)-enriched chiralities, associated with three DNA sequences. The dependence of PCR efficiency on the concentration of DNA:SWCNT preparations was measured, as well as their age and level of dispersion (less than one month or between four and ten months). Additionally, the ability to directly amplify the DNA sequence associated with the SWCNT scaffold was investigated. In PCRs with DNA:SWCNT preparations less than one month old, concentrations greater than or equal to 0.1 mg/mL inhibited the PCR reaction. In PCRs with older preparations, no inhibition was seen at 0.01 or 0.1 mg/mL, with amplification at 1 mg/mL in some samples. Additionally, our studies showed that the DNA directly associated with the SWCNT can be amplified using PCR. This work provides an inhibitory concentration of DNA-dispersed SWCNT in PCR reactions for different preparations as well as a basis for future DNA:SWCNT studies that require PCR amplification. This will be useful for future studies focused on the use of SWCNT in molecular sensing technologies.
Comparison of RTN and TDDS methods for trap extraction in trigate nanowires

In this paper we present a direct comparison of the two basic techniques for trap extraction, the Random Telegraph Noise (RTN) and the Time Dependent Defect Spectroscopy (TDDS). By using the method of histograms, extracted from the measured drain current transients, we divided the recorded defects in three different categories. Results show that we night be able to detect traps deeper in the oxide and, also, near the dielectric/channel interface. As we scale down, we found a better correlation between the two methods, while the after stress results show a merging of the slopes compared to the bimodal distribution that appeared at the beginning.
Comparison of immune regulatory factors in acute and chronic lesions of cutaneous leishmaniasis due to Leishmania major

Background: Adaptive immune response is an important factor in the healing process and development of protection in cutaneous leishmaniasis (CL). Little information is available in human CL about the importance of the balance between effector and regulatory immune responses. Therefore, the aim of this study was to asses messenger ribonucleic acid (mRNA) expression of interleukin-10 (IL-10), IL-4, transforming growth factor-β1 (TGF-β1), interferon-g (IFN-γ), and forkhead box P3 (Foxp3) (as a marker of regulatory T cells) in acute and chronic CL lesions caused by Leishmania major compared with normal skin samples. Materials and Methods: Thirty biopsies were obtained from CL patients with acute lesions (AL, n = 13), chronic lesions (CH, n = 11) and healthy volunteers (n = 6). Relative expressions of target genes were determined by means of reverse transcription real time polymerase chain reaction and were compared with the controls. Results: Expression of Foxp3, IL-4, and IFN-γ were significantly more in CH than AL group of patients (Foxp3: Median 0.48, inter-quartile range 0.32-0.76 [arbitrary units] for AL, and 0.97 (0.75-1.30) for CH, P = 0.006; IFN-γ: 45.98 (33.39-173.48) for AL, and 200.53 (97.49-361.76) for CH, P = 0.023; IL-4: 0.49 (0.34-2.16) for AL, and 2.14 (1.30-7.11) for CH, P = 0.021). Expression of TGF-β was not significantly different between groups. Conclusion: The results indicate that IL-4 secretion at the site of L. major infection rather than low IFN-γ production might have a role in prolongation of disease. Despite a moderate increase of Foxp3 expression in chronic lesions, function of Tregs in persistent infection is not clear.
Speech Summarization: An Approach through Word Extraction and a Method for Evaluation

SUMMARY In this paper, we propose a new method of automatic speech summarization for each utterance, where a set of words that maximizes a summarization score is extracted from automatic speech transcriptions. The summarization score indicates the appropriateness of summarized sentences. This extraction is achieved by using a dynamic programming technique according to a target summarization ratio. This ratio is the number of characters/words in the summarized sentence divided by the number of characters/words in the originalsentence. The extracted set of words is then connected to build a summarized sentence. The summarization score consists of a word significance measure, linguistic likelihood, and a confidence measure. This paper also proposes a new method of measuring summarization accuracy based on a word network expressing manualsummarization results. The summarization accuracy of each automatic summarization is calculated by comparing it with the most similar word string in the network. Japanese broadcast-news speech, transcribed using a large-vocabulary continuous-speech recognition (LVCSR) system, is summarized and evaluated using our proposed method with 20, 40, 60, 70 and 80% summarization ratios. Experimentalresul ts revealthat the proposed method can effectively extract relatively important information by removing redundant or irrelevant information.
Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

RNA biomarkers discovered by RT-PCR-based gene expression profiling of archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for widely used clinical diagnostic tests; however, RT-PCR is practically constrained in the number of transcripts that can be interrogated. We have developed and optimized RNA-Seq library chemistry as well as bioinformatics and biostatistical methods for whole transcriptome profiling from FFPE tissue. The chemistry accommodates low RNA inputs and sample multiplexing. These methods both enable rediscovery of RNA biomarkers for disease recurrence risk that were previously identified by RT-PCR analysis of a cohort of 136 patients, and also identify a high percentage of recurrence risk markers that were previously discovered using DNA microarrays in a separate cohort of patients, evidence that this RNA-Seq technology has sufficient precision and sensitivity for biomarker discovery. More than two thousand RNAs are strongly associated with breast cancer recurrence risk in the 136 patient cohort (FDR <10%). Many of these are intronic RNAs for which corresponding exons are not also associated with disease recurrence. A number of the RNAs associated with recurrence risk belong to novel RNA networks. It will be important to test the validity of these novel associations in whole transcriptome RNA-Seq screens of other breast cancer cohorts.
Quantitative assessment of pupillary light reflex in normal and anesthetized dogs: a preliminary study

The purpose of this study was to quantitatively assess the pupillary light reflex (PLR) in normal and anesthetized dogs using a pupillometer. Eleven dogs (20 eyes) of various breeds were included. PLRs were measured with a handheld pupillometer in dim light before and during anesthesia. Anesthesia was conducted with atropine, xylazine and ketamine. Parameters of pupillometry included neurological pupil index (NPi), pupil size, percent of change (%CH), latency (LAT), constriction velocity (CV), maximum constriction velocity (MCV) and dilation velocity (DV). NPi,%CH, CV and MCV were significantly decreased during anesthesia compared with the pre-anesthesia data. The results suggest that atropine-xylazine-ketamine combination anesthesia depresses the PLR. Additionally, this study demonstrates the feasibility of the use of a pupillometer in dogs.
Thrombolysis vs. bleeding from hemostatic sites by a prourokinase mutant compared with tissue plasminogen activator

Summary. Background: A single site mutant (M5) of prourokinase (proUK) was developed to make proUK less vulnerable to spontaneous activation in plasma. This was a problem that seriously compromised proUK in clinical trials, as it precluded proUK‐mediated fibrinolysis at therapeutic concentrations. Methods and results: After completing dose‐finding studies, 12 anesthetized dogs with femoral artery thrombosis were given either M5 (2.0 mg kg−1) or tissue plasminogen activator (t‐PA) (1.4 mg kg−1) by i.v. infusion over 60 min (20% administered as a bolus). Two pairs of standardized injuries were inflicted at which hemostasis was completed prior to drug administration. Blood loss was quantified by measuring the hemoglobin in blood absorbed from these sites. Thrombolysis was evaluated at 90 min and was comparably effective by both activators. Rethrombosis developed in one t‐PA dog. The principal difference found was that blood loss was 10‐fold higher with t‐PA (mean ∼40 mL) than with M5 (mean ∼4 mL) (P = 0.026) and occurred at more multiple sites (mean 2.7 vs. 1.2). This effect was postulated to be related to differences in the mechanism of plasminogen activation by t‐PA and M5 in which the latter is promoted by degraded rather than intact (hemostatic) fibrin. In addition, two‐chain M5 was efficiently inactivated by plasma C1 inactivator, an exceptional property which helped contain its non‐specific proteolytic effect. Conclusions: Intravascular thrombolysis by M5 was accompanied by significantly less bleeding from hemostatic sites than by t‐PA. This was attributed to the proUK paradigm of fibrinolysis being retained at therapeutic concentrations by the mutation.
Paleontology of Early Cretaceous deep-water samples dredged from the Wallaby Plateau: new perspectives of Gondwana break-up along the Western Australian margin

Sedimentary and paleontological samples from steep, deep-water escarpments of the Wallaby Plateau, 400 km west of Carnarvon, Western Australia, represent the first collected soft-rock geological data from this immense bathymetric high. The study of this vast marginal plateau of 100 000 km2 has been hampered by a paucity of rock data arising from difficulties in sampling in water depths of 2200–5700 m. Only modern carbonate, altered tholeiitic basalts and volcaniclastic rocks have been recorded previously. Variably fossiliferous to unfossiliferous claystone, siltstone and sandstone samples from 12 southern Wallaby Plateau stations (3015–5159 m water depths) range from interpreted paralic to shallow-water marine settings, and contain low to moderately diverse assemblages of Bivalvia, Gastropoda, Ostracoda, Foraminifera, palynomorphs, very rare nannofossils, and teleost fish fragments, which collectively point to an age range of latest Berriasian to Barremian–Aptian in the Early Cretaceous. This age range pre-dates, straddles and post-dates the breakup and opening of the Cuvier Abyssal Plain. Seismic imaging of the Wallaby Plateau exhibits a substantial thickness of both dipping and flat-lying, sub-parallel reflectors beneath parts of the Lower Cretaceous Gondwanan breakup unconformity. This information, taken together with the recent identification of Oxfordian–Kimmeridgian Foraminifera from the same location, indicates the presence of a pre-breakup sedimentary section beneath parts of the Wallaby Plateau.