Miracle-dz/UniFAR-FTUs huggingface dataset:
Recording and quantification of ultrasonic echolocation clicks from free-ranging toothed whales

Toothed whales produce short, ultrasonic clicks of high directionality and source level to probe their environment acoustically. This process, termed echolocation, is to a large part governed by the properties of the emitted clicks. Therefore derivation of click source parameters from free-ranging animals is of increasing importance to understand both how toothed whales use echolocation in the wild and how they may be monitored acoustically. This paper addresses how source parameters can be derived from free-ranging toothed whales in the wild using calibrated multi-hydrophone arrays and digital recorders. We outline the properties required of hydrophones, amplifiers and analog to digital converters, and discuss the problems of recording echolocation clicks on the axis of a directional sound beam. For accurate localization the hydrophone array apertures must be adapted and scaled to the behavior of, and the range to, the clicking animal, and precise information on hydrophone locations is critical. We provide examples of localization routines and outline sources of error that lead to uncertainties in localizing clicking animals in time and space. Furthermore we explore approaches to time series analysis of discrete versions of toothed whale clicks that are meaningful in a biosonar context. r 2007 Elsevier Ltd. All rights reserved.
In vivo visualization of Candida albicans infections

Candida yeasts are commensals of human skin and mucosal surfaces but can also cause fungal infections. Candida albicans is a major fungal pathogen and causes life-threatening diseases especially but not limited to immuno-compromised patients. Candidiasis most often develops in the mouth or throat (called oropharyngeal candidiasis or thrush), the vagina (yeast infection) or as invasive candidiasis after entering the bloodstream and thus spreading throughout the body (Brown et al., 2012).
IVIg Promote Cross-Tolerance against Inflammatory Stimuli In Vitro and In Vivo

IVIg is an approved therapy for immunodeficiency and for several autoimmune and inflammatory diseases. However, the molecular basis for the IVIg anti-inflammatory activity remains to be fully explained and cannot be extrapolated from studies on animal models of disease. We now report that IVIg impairs the generation of human monocyte–derived anti-inflammatory macrophages by inducing JNK activation and activin A production and limits proinflammatory macrophage differentiation by inhibiting GM-CSF–driven STAT5 activation. In vivo, IVIg provokes a rapid increase in peripheral blood activin A, CCL2, and IL-6 levels, an effect that can be recapitulated in vitro on human monocytes. On differentiating monocytes, IVIg promotes the acquisition of altered transcriptional and cytokine profiles, reduces TLR expression and signaling, and upregulates negative regulators of TLR-initiated intracellular signaling. In line with these effects, in vivo IVIg infusion induces a state tolerant toward subsequent stimuli that results in reduced inflammatory cytokine production after LPS challenge in human peripheral blood and significant protection from LPS-induced death in mice. Therefore, IVIg conditions human macrophages toward the acquisition of a state of cross-tolerance against inflammatory stimuli, an effect that correlates with the net anti-inflammatory action of IVIg in vivo.
A critical threshold for design effects in network sampling

Web crawling, snowball sampling, and respondent-driven sampling (RDS) are three types of network sampling techniques used to contact individuals in hard-to-reach populations. This paper studies these procedures as a Markov process on the social network that is indexed by a tree. Each node in this tree corresponds to an observation and each edge in the tree corresponds to a referral. Indexing with a tree (instead of a chain) allows for the sampled units to refer multiple future units into the sample. In survey sampling, the design effect characterizes the additional variance induced by a novel sampling strategy. If the design effect is some value DE, then constructing an estimator from the novel design makes the variance of the estimator DE times greater than it would be under a simple random sample with the same sample size n . Under certain assumptions on the referral tree, the design effect of network sampling has a critical threshold that is a function of the referral rate m and the clustering structure in the social network, represented by the second eigenvalue of the Markov transition matrix, λ 2 . If m < 1 /λ 22 , then the design effect is ﬁnite (i.e., the standard estimator is √ n -consistent). However, if m > 1 /λ 22 , then the design effect grows with n (i.e., the standard estimator is no longer √ n -consistent). Past this critical threshold, the standard error of the estimator converges at the slower rate of n log m λ 2 . The Markov model allows for nodes to be resampled; computational results show that the ﬁndings hold in without-replacement sampling. To estimate conﬁdence intervals that adapt to the correct level of uncertainty, a novel resampling procedure is proposed. Computational experiments compare this procedure to previous techniques.
Determinants of Male Spacing Behaviour in Panacanthus pallicornis (Orthoptera: Tettigoniidae)

Panacanthus pallicornis is a neotropical species of katydid endemic to Colombia that inhabits premontane forests, and individuals are found in regenerating (RF) and dense forest (DF) habits. Members of this species are made conspicuous by their colouration, remarkable defensive body thorns and the loud mating calls of the males. Through capture, marking, and recapture, we determined singing-site characteristics in two different natural habitats: an RF and a DF. Using nearest neighbour analysis, we found male distribution tends to uniformity in forest habitats, but in the RF, male distribution is more random. Males also showed preference for high singing sites and these were correlated with host plant height. Although host plants in DF were taller than those in the RF, male’s perch preference was independent from the habitat; and in RF, males select lower perches. To investigate if male spacing was a function of the calling song, we manipulated two groups of males from a different population, one group deafened (tympanic membranes torn), and another control group with tympanic membranes intact. Insects were released from a single location in the two different zones of similar area. After a number of days we measured male displacement, and found that the deafened group distribution tended to aggregation, while the control group spread throughout the experimental zone with a random distribution. These results suggest that male spacing behaviour is one of the functions of the calling song. Based on a pre-established phylogenetic framework of the genus Panacanthus, we discuss some implications for the evolution of the calling song of P. pallicornis in both RF and DF.
Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor

Stress-induced adaptations require multiple levels of regulation in all organisms to repair cellular damage. In the present study we evaluated the genome-wide transcriptional and translational changes following heat stress exposure in the soil-dwelling model actinomycete bacterium, Streptomyces coelicolor. The combined analysis revealed an unprecedented level of translational control of gene expression, deduced through polysome profiling, in addition to transcriptional changes. Our data show little correlation between the transcriptome and ‘translatome’; while an obvious downward trend in genome wide transcription was observed, polysome associated transcripts following heat-shock showed an opposite upward trend. A handful of key protein players, including the major molecular chaperones and proteases were highly induced at both the transcriptional and translational level following heat-shock, a phenomenon known as ‘potentiation’. Many other transcripts encoding cold-shock proteins, ABC-transporter systems, multiple transcription factors were more highly polysome-associated following heat stress; interestingly, these protein families were not induced at the transcriptional level and therefore were not previously identified as part of the stress response. Thus, stress coping mechanisms at the level of gene expression in this bacterium go well beyond the induction of a relatively small number of molecular chaperones and proteases in order to ensure cellular survival at non-physiological temperatures.
Suppression of External NADPH Dehydrogenase—NDB1 in Arabidopsis thaliana Confers Improved Tolerance to Ammonium Toxicity via Efficient Glutathione/Redox Metabolism

Environmental stresses, including ammonium (NH4+) nourishment, can damage key mitochondrial components through the production of surplus reactive oxygen species (ROS) in the mitochondrial electron transport chain. However, alternative electron pathways are significant for efficient reductant dissipation in mitochondria during ammonium nutrition. The aim of this study was to define the role of external NADPH-dehydrogenase (NDB1) during oxidative metabolism of NH4+-fed plants. Most plant species grown with NH4+ as the sole nitrogen source experience a condition known as “ammonium toxicity syndrome”. Surprisingly, transgenic Arabidopsis thaliana plants suppressing NDB1 were more resistant to NH4+ treatment. The NDB1 knock-down line was characterized by milder oxidative stress symptoms in plant tissues when supplied with NH4+. Mitochondrial ROS accumulation, in particular, was attenuated in the NDB1 knock-down plants during NH4+ treatment. Enhanced antioxidant defense, primarily concerning the glutathione pool, may prevent ROS accumulation in NH4+-grown NDB1-suppressing plants. We found that induction of glutathione peroxidase-like enzymes and peroxiredoxins in the NDB1-surpressing line contributed to lower ammonium-toxicity stress. The major conclusion of this study was that NDB1 suppression in plants confers tolerance to changes in redox homeostasis that occur in response to prolonged ammonium nutrition, causing cross tolerance among plants.
IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts

Significance Reliable proteome-wide quantification in large biological cohorts is highly valuable for clinical and pharmaceutical research yet remains extremely challenging despite recent technical advancements. Specifically, elevated missing data levels and compromised quantitative quality are common issues for prevalent methods. Here, we describe an IonStar technique taking advantage of sensitive and selective MS1 ion current-base quantification via innovations in effective and reproducible quantitative feature generation. Compared with several label-free strategies, IonStar showed superior performance in large-cohort analysis, manifested by excellent accuracy/precision, extremely low missing data, and confident discovery of subtle protein changes. In a proof-of-concept study, we demonstrated that IonStar quantified >7,000 unique proteins in 100 brain samples with no missing data and excellent quantitative quality, which has not been achievable by existing methods. Reproducible quantification of large biological cohorts is critical for clinical/pharmaceutical proteomics yet remains challenging because most prevalent methods suffer from drastically declined commonly quantified proteins and substantially deteriorated quantitative quality as cohort size expands. MS2-based data-independent acquisition approaches represent tremendous advancements in reproducible protein measurement, but often with limited depth. We developed IonStar, an MS1-based quantitative approach enabling in-depth, high-quality quantification of large cohorts by combining efficient/reproducible experimental procedures with unique data-processing components, such as efficient 3D chromatographic alignment, sensitive and selective direct ion current extraction, and stringent postfeature generation quality control. Compared with several popular label-free methods, IonStar exhibited far lower missing data (0.1%), superior quantitative accuracy/precision [∼5% intragroup coefficient of variation (CV)], the widest protein abundance range, and the highest sensitivity/specificity for identifying protein changes (<5% false altered-protein discovery) in a benchmark sample set (n = 20). We demonstrated the usage of IonStar by a large-scale investigation of traumatic injuries and pharmacological treatments in rat brains (n = 100), quantifying >7,000 unique protein groups (>99.8% without missing data across the 100 samples) with a low false discovery rate (FDR), two or more unique peptides per protein, and high quantitative precision. IonStar represents a reliable and robust solution for precise and reproducible protein measurement in large cohorts.
The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium

Maintenance of a quiescent and organotypically-differentiated layer of blood vessel-lining endothelial cells (EC) is vital for human health. Yet, the molecular mechanisms of vascular quiescence remain largely elusive. Here we identify the genome-wide transcriptomic program controlling the acquisition of quiescence by comparing lung EC of infant and adult mice, revealing a prominent regulation of TGFß family members. These transcriptomic changes are distinctly accompanied by epigenetic modifications, measured at single CpG resolution. Gain of DNA methylation affects developmental pathways, including NOTCH signaling. Conversely, loss of DNA methylation preferentially occurs in intragenic clusters affecting intronic enhancer regions of genes involved in TGFβ family signaling. Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation.
MicroRNA-125b inhibits cell proliferation and induces cell apoptosis in esophageal squamous cell carcinoma by targeting BMF

MicroRNAs (miRNAs) have been reported to regulate the expression of genes by suppressing translation or facilitating mRNA decay. Their expression regulates a wide variety of cellular processes, including the development and progression of cancer. Esophageal squamous cell carcinoma (ESCC) is a malignant cancer with high morbidity and recurrence in Asia. In the present study, the biological function of miR-125b and its underlying mechanism in ESCC were explored. The results revealed that miR-125b expression was significantly decreased in ESCC tissues and cell lines. A decrease in miR-125b was markedly related to lymphatic metastasis in patients. Functional analysis revealed that the overexpression of miR-125b using miR-125b mimics significantly inhibited cell growth and induced cell apoptosis, and increased the G1 phase of the cell cycle in EC109 and EC9706 cells. Notably, the miR-125b inhibitors revealed the opposite effect. Additionally, overexpression of miR-125b significantly inhibited tumor growth in vivo. Furthermore, BCL-2-modifying factor (BMF) was considered to be a potential candidate target of miR-125b based on miRNA target databases. miR-125b negatively regulated BMF expression by directly binding to its 3′-untranslated region. BMF was a functional target of miR-125b in the regulation of cell proliferation, cell apoptosis and the cell cycle in EC109 and EC9706 cells. In clinical ESCC specimens, BMF expression was upregulated, and negatively correlated with that of miR-125b. In conclusion, miR-125b had an antitumor role in ESCC cells mediated by targeting BMF, which can be potentially useful for tumorigenesis in ESCC.
Expansionary Austerity New International Evidence

This paper investigates the short-term effects of fiscal consolidation on economic activity in OECD economies. We examine the historical record, including Budget Speeches and IMFdocuments, to identify changes in fiscal policy motivated by a desire to reduce the budget deficit and not by responding to prospective economic conditions. Using this new dataset, our estimates suggest fiscal consolidation has contractionary effects on private domestic demand and GDP. By contrast, estimates based on conventional measures of the fiscal policy stance used in the literature support the expansionary fiscal contractions hypothesis but appear to be biased toward overstating expansionary effects.
Retrieving Essential Material at the End of Lectures Improves Performance on Statistics Exams

At the end of each lecture in a statistics for psychology course, students answered a small set of questions that required them to retrieve information from the same day’s lecture. These exercises constituted retrieval practice for lecture material subsequently tested on four exams throughout the course. This technique is called the PUREMEM (pronounced “pure mem”) procedure for Pure Memory or Practicing Unassisted Retrieval to Enhance Memory for Essential Material. Exam scores were significantly and substantially higher in a section of the course taught with the PUREMEM procedure than one taught without it. Students liked the procedure and believed it increased learning via several different mechanisms.
Profound consequences of hidradenitis suppurativa: a review

Hidradenitis suppurativa (HS) influences patients’ lives in many ways. The most troublesome symptom of HS is chronic pain, of mild‐to‐moderate intensity, which is reported by almost all patients. With reference to psychosocial evaluation, HS appears to be a highly debilitating disease. The major factors influencing patients’ well‐being are disease severity, the number of flares or affected skin areas, and the lesion location. The mean Dermatology Life Quality Index scores of 8·3–12·7 points obtained among patients with HS are typical for severe dermatoses, which have a large impact on patients’ quality of life (QoL). HS not only affects skin‐related QoL issues, but also has a profound impact on general QoL measures – it causes substantial deterioration of both physical and mental health. Considering the impaired QoL due to HS and HS‐associated, nonpsychiatric comorbidities, it is not surprising that patients with HS experience psychological disturbances. In both observational and registry studies, depression and anxiety were significantly related to HS. The prevalences were estimated as 1·6–42·9% and 0·8–3·9%, respectively. HS was also linked to feelings of loneliness and stigmatization. Moreover, these patients have a significantly increased suicide risk (hazard ratio 2·42). HS, with its frequent involvement of the genital area, causes a pronounced impairment of sex life (66·7% of patients with HS reported sexual difficulties). Finally, HS causes significant financial burden, not only through the costs of healthcare, but also due to a substantial impact on patients’ professional careers. This is a reason for absenteeism from work for approximately half of patients, and a relatively high unemployment rate.
Business Cycle, Great Recession and Part-time Jobs

During the Great Recession, the U.S. economy witnessed a substantial rise in part-time employment for sustained periods. We extend the New Keynesian-unemployment model by Gali et al. (2012) to allow substitution between full-time and part-time labor and estimate the model's parameters using the Bayesian method. In our model, households and firms can optimally allocate full-time and part-time labor. Moreover, disturbances exist in part-time labor supply (household disutility in part-time labor) and part-time labor demand (firms' efficiency to utilize part-time labor). Although several shocks were found to cause the transition to part-time jobs during the recession, the most important factor was the part-time labor supply shock that increases part-time participation. The transition from full-time to part-time jobs, caused by part-time labor market shocks, mitigated the contraction in output during the recession. Part-time labor supply shock also explains a significant portion of slow recovery in gross wage during the recession, as the shock lowers part-time wage as well as the proportion of full-time workers in total employment.
Emotional Pain and Acute Nociception

Emotional Pain and Acute Nociception Alison M. Vargovich This study examined differences and similarities in responses to acute nociception in adults with a significant history of emotional pain relative to matched controls with a significant past positive life experience and a sample of chronic pain patients. Using 28 volunteers who responded to advertisements (n = 14, emotional pain group; n = 14, positive life experience group), and 14 chronic pain patients from a prior study, this investigation utilized measures of pain threshold and tolerance during a laboratory finger pressure pain induction experiment. Each participant experienced two levels of pressure pain (i.e., high and low) and two levels of induced fear (i.e., high and low). Mixed between-within subject ANOVAs revealed a significant main effect of weight for pain threshold and tolerance, suggesting the importance of stimulus intensity. Exploratory analyses suggested an interaction between weight and group membership for pain tolerance. Findings indicate that individuals who are self-selected to talk about emotional pain possibly may have a higher pain tolerance for more intense pain stimulation as compared to participants reporting positive life events and chronic pain. Acute Nociception iii Acknowledgements The completion of this thesis project came with a lot of support, guidance, and help from others. I would like to begin by thanking my committee members, Kevin Larkin and Aaron Metzger, for their helpful comments and suggestions. To my mentor, committee chair, and friend Dan McNeil, without your support and guidance I would not have been able to complete this project or learn so much about research and myself. I want to thank all those in the Anxiety, Psychophysiology, and Pain Research Laboratory in the Department of psychology at West Virginia University who helped with my data collection, especially Cameron Randall and Grant Shulman. You both made the many hours of data collection much more fun and enjoyable. Finally, I would not be the person I am without the influence of my family. To my parents, Paul and Suzanne, thank you for your constant love and support throughout my entire life. You have a funny way of encouraging me to persevere and have fun; work hard, play hard. Your dedication to our family is an inspiration and I miss you every day. To my Grandma Millie, the heart of our family, your kindness and love never fail to lift my spirits. To my siblings, Angela, Paul, Lisa, and Lauren, thanks for making me laugh and always reminding me that I still am the baby, no matter my age or degree. I love you all, and all of your little ones. Lastly, I would like to thank my friend and love, Mark, for his support and impeccable sense of humor. You help me to put things into perspective and never let me take myself too seriously. Acute Nociception iv Table of