Miracle-dz/UniFAR-FTUs huggingface dataset:
Widespread Misinterpretable ChIP-seq Bias in Yeast

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to detect genome-wide interactions between a protein of interest and DNA in vivo. Loci showing strong enrichment over adjacent background regions are typically considered to be sites of binding. Insufficient attention has been given to systematic artifacts inherent to the ChIP-seq procedure that might generate a misleading picture of protein binding to certain loci. We show here that unrelated transcription factors appear to consistently bind to the gene bodies of highly transcribed genes in yeast. Strikingly, several types of negative control experiments, including a protein that is not expected to bind chromatin, also showed similar patterns of strong binding within gene bodies. These false positive signals were evident across sequencing platforms and immunoprecipitation protocols, as well as in previously published datasets from other labs. We show that these false positive signals derive from high rates of transcription, and are inherent to the ChIP procedure, although they are exacerbated by sequencing library construction procedures. This expression bias is strong enough that a known transcriptional repressor like Tup1 can erroneously appear to be an activator. Another type of background bias stems from the inherent nucleosomal structure of chromatin, and can potentially make it seem like certain factors bind nucleosomes even when they don't. Our analysis suggests that a mock ChIP sample offers a better normalization control for the expression bias, whereas the ChIP input is more appropriate for the nucleosomal periodicity bias. While these controls alleviate the effect of the biases to some extent, they are unable to eliminate it completely. Caution is therefore warranted regarding the interpretation of data that seemingly show the association of various transcription and chromatin factors with highly transcribed genes in yeast.
Infant discrimination of humanoid robots

Recently, extremely humanlike robots called “androids” have been developed, some of which are already being used in the field of entertainment. In the context of psychological studies, androids are expected to be used in the future as fully controllable human stimuli to investigate human nature. In this study, we used an android to examine infant discrimination ability between human beings and non-human agents. Participants (N = 42 infants) were assigned to three groups based on their age, i.e., 6- to 8-month-olds, 9- to 11-month-olds, and 12- to 14-month-olds, and took part in a preferential looking paradigm. Of three types of agents involved in the paradigm—a human, an android modeled on the human, and a mechanical-looking robot made from the android—two at a time were presented side-by-side as they performed a grasping action. Infants’ looking behavior was measured using an eye tracking system, and the amount of time spent focusing on each of three areas of interest (face, goal, and body) was analyzed. Results showed that all age groups predominantly looked at the robot and at the face area, and that infants aged over 9 months watched the goal area for longer than the body area. There was no difference in looking times and areas focused on between the human and the android. These findings suggest that 6- to 14-month-olds are unable to discriminate between the human and the android, although they can distinguish the mechanical robot from the human.
The effects of sensory hearing loss on cochlear filter times estimated from auditory brainstem response latencies.

Derived-band auditory brainstem responses (ABRs) were obtained in 43 normal-hearing and 80 cochlear hearing-impaired individuals using clicks and high-pass noise masking. The response times across the cochlea [the latency difference between wave V's of the 5.7- and 1.4-kHz center frequency (CF) derived bands] were calculated for five levels of click stimulation ranging from 53 to 93 dB p.-p.e. SPL (23 to 63 dB nHL) in 10-dB steps. Cochlear response times appeared to shorten significantly with hearing loss, especially when the average pure tone (1 to 8 kHz) hearing loss exceeded 30 dB. Examination of derived-band latencies indicates that this shortening is due to a dramatic decrease of wave V latency in the lower CF derived band. Estimates of cochlear filter times in terms of the number of periods to maximum response (Nmax) were calculated from derived-band latencies corrected for gender-dependent cochlear transport and neural conduction times. Nmax decreased as a function of hearing loss, especially for the low CF derived bands. The functions were similar for both males and females. These results are consistent with broader cochlear tuning due to peripheral hearing loss. Estimating filter response times from ABR latencies enhances objective noninvasive diagnosis and allows delineation of the differential effects of pathology on the underlying cochlear mechanisms involved in cochlear transport and filter build-up times.
Multiwavelength studies of the Seyfert 1 galaxy NGC 7469 II. X-ray and UV observations with XMM-Newton

We present an XMM-Newton observation of NGC 7469, including studies of the X-ray and UV variability, 0.2 10 keV spectral continuum, Fe K emission line and the first-ever high-resolution X-ray spectrum of the soft X-ray warm absorber. We compare the properties of this X-ray warm absorber with the UV warm absorber as seen in a FUSE ob- servation one year previously. The 0.2 10 keV spectral continuum is best fitted by a power-law plus two blackbody model. An Fe K emission line is visible which consists of a single narrow component and is well-modelled by a simple Gaussian. Narrow absorption and emission lines in the soft X-ray RGS spectrum demonstrate the existence of a multi-phase warm ab- sorber with a range in log of 2t o 2w here is in erg cm s 1 . The warm absorber is blueshifted by several hundred km s 1 . The highest-ionisation phase of the absorber is the best constrained and has an overall equivalent Hydrogen column of order 10 20 cm 2 ; we find that its ionisation parameter is consistent with that of the warm emitter which generates the narrow emission lines. We identify this high ionisation absorber with the low-velocity phase of the UV absorber observed by FUSE.
Vowel height is intimately associated with stress accent in spontaneous american English discourse

There is a systematic relationship between stress accent and vocalic identity in spontaneous English discourse (the Switchboard corpus of telephone dialogues). Low vowels are much more likely to be fully accented than their high vocalic counterparts. And conversely, high vowels are far more likely to lack stress accent than low or mid vocalic segments. Such patterns imply that stress accent and vowel height are bound together at some level of lexical representation. Vocalic duration appears to be the primary acoustic cue associated with stress accent, and the association between vowel height and accent level is most clearly observed in this dimension, particularly for diphthongs and the low, tense monophthongs. Together, the data suggest that vocalic duration plays an exceedingly important role in understanding spoken language.
Resonance tube phonation in water: High-speed imaging, electroglottographic and oral pressure observations of vocal fold vibrations - a pilot study

Phonation into glass tubes (‘resonance tubes’), keeping the free end of the tube in water, has been a frequently used voice therapy method in Finland and more recently also in other countries. The purpose of this exploratory study was to investigate what effects tube phonation with and without water has on the larynx. Two participants were included in the study. The methods used were high-speed imaging, electroglottographic observations of vocal fold vibrations, and measurements of oral pressure during tube phonation. Results showed that the fluctuation in the back pressure during tube phonation in water altered the vocal fold vibrations. In the high-speed imaging, effects were found in the open quotient and amplitude variation of the glottal opening. The open quotient increased with increasing water depth (from 2 cm to 6 cm). A modulation effect by the water bubbles on the vocal fold vibrations was seen both in the high-speed glottal area tracings and in the electroglottography signal. A second experiment revealed that the increased average oral pressure was largely determined by the water depth. The increased open quotient can possibly be explained by an increased abduction of the vocal folds and/or a reduced transglottal pressure. The back pressure of the bubbles also modulates glottal vibrations with a possible ‘massage’ effect on the vocal folds. This effect and the well-defined average pressure increase due to the known water depth are different from those of other methods using a semi-occluded vocal tract.
Effects of terrigenous sediment on settlement and survival of the reef coral Pocillopora damicornis

Survival and settlement of Pocillopora damicornis larvae on hard surfaces covered with fine (<63 µm) terrigenous red clay was measured in laboratory Petri dishes. The dishes were prepared with sediment films of various thicknesses covering the bottoms. Coral larvae were incubated in the dishes for two weeks and the percent that settled on the bottom was determined. There was a statistically significant relationship between the amount of sediment and coral recruitment on the bottom, with no recruitment on surfaces having a sediment cover above 0.9 mg cm−2. Experimental conditions for the delicate coral larvae were favorable in these experiments. Total survival over the two week settlement tests expressed as the sum of coral recruits and live larvae at the end of the experiment did not show a significant decline, so the major impact of the sediment was on successful settlement rather than on mortality. Larval substrate selection behavior was the primary factor in the observed result.
Modulation of Self-Esteem in Self- and Other-Evaluations Primed by Subliminal and Supraliminal Faces

Background Past research examining implicit self-evaluation often manipulated self-processing as task-irrelevant but presented self-related stimuli supraliminally. Even when tested with more indirect methods, such as the masked priming paradigm, participants' responses may still be subject to conscious interference. Our study primed participants with either their own or someone else's face, and adopted a new paradigm to actualize strict face-suppression to examine participants' subliminal self-evaluation. In addition, we investigated how self-esteem modulates one's implicit self-evaluation and validated the role of awareness in creating the discrepancy on past findings between measures of implicit self-evaluation and explicit self-esteem. Methodology/Principal Findings Participants' own face or others' faces were subliminally presented with a Continuous Flash Suppression (CFS) paradigm in Experiment 1, but supraliminally presented in Experiment 2, followed by a valence judgment task of personality adjectives. Participants also completed the Rosenberg Self-Esteem Scale in each experiment. Results from Experiment 1 showed a typical bias of self-positivity among participants with higher self-esteem, but only a marginal self-positivity bias and a significant other-positivity bias among those with lower self-esteem. However, self-esteem had no modulating effect in Experiment 2: All participants showed the self-positivity bias. Conclusions/Significance Our results provide direct evidence that self-evaluation manifests in different ways as a function of awareness between individuals with different self-views: People high and low in self-esteem may demonstrate different automatic reactions in the subliminal evaluations of the self and others; but the involvement of consciousness with supraliminally presented stimuli may reduce this dissociation.
Mediastinal tumor size and response to chemotherapy are the only prognostic factors in supradiaphragmatic Hodgkin's disease treated by ABVD plus radiotherapy: ten-year results of the Paris-Ouest-France 81/12 trial, including 262 patients.

PURPOSE To identify prognostic factors in 262 patients with supradiaphragmatic Hodgkin's disease (HD), clinical stages (CS) I and II, prospectively treated between 1981 and 1988 according to the Paris-Ouest-France (POF) 81/12 protocol by three 1-month cycles of doxorubicin, bleomycin, vinblastine, and dacarbazine plus methylprednisone (ABVD-MP) followed by subtotal nodal irradiation (RT). PATIENTS AND METHODS The size of mediastinal tumor (MT) was measured in all patients: 66 did not have MT (NoMT); 105 had a small-size MT (SSMT), ie, mediastinal mass ratio (MMR) less than 0.33; 58 had a medium-size MT (MSMT), ie, MMR > or = 0.33 and less than 0.45; and 33 had a bulky MT (BuMT), ie, MMR > or = 0.45. All patients received three cycles (CS IA, one cycle only) of ABVD-MP; patients in partial remission (PR) or complete remission (CR) after chemotherapy (CT) received supradiaphragmatic RT (involved fields, 40 Gy; adjacent fields, 30 Gy) plus lumboaortic and splenic RT (30 Gy); patients not in CR or PR after CT received salvage CT. RESULTS Two hundred seventeen patients (82.8%) entered CR after CT and 258 (98.5%) after RT. Ten-year freedom-from-progression (FFP) and survival rateswere 88.6% and 89.4%, respectively. According to univariate analysis, MT size and post-CT status were the only factors to influence both FFP and survival. For patients with NoMT or SSMT, those with MSMT, and those with BuMT, FFP rates were 94.1%, 87.0%, and 63.0% (P < .001), respectively, while corresponding survival rates were 92.6%, 87.2%, and 78.2% (P < .05). FFP rates were significantly different between the patients who achieved CR and those who did not achieve CR after CT: 94.6% versus 65.3% (P < .001); corresponding survival rates were 89.9% and 73.7% (P < .01). Multivariate analysis confirmed that MT size and post-CT status were the only two prognostic factors for FFP; for survival, the same two characteristics, as well as age (< 40 v > or = 40 years), significantly affected prognosis. We were thus able to identify three groups. The 33 patients (12.6%) with a BuMT had 10-year FFP and survival rates of 63.0% and 78.2%, respectively. Of 229 patients without BuMT, the 195 who attained CR after CT had an optimal prognosis (FFP, 96.6%; survival, 93.6%), while those who failed to achieve CR after CT had an intermediate prognosis (FFP, 68.8%; survival, 77.6%). CONCLUSION These results demonstrate the independent impact on HD prognosis of tumor burden and post-CT status.
Studies of the cat's medial interlaminar nucleus: A subdivision of the dorsal lateral geniculate nucleus

The medial interlaminar nucleus (MIN) of the cat lies medial to the laminated region of the dorsal lateral geniculate (lamLGN). This latter region includes the A and C laminae. As does lamLGN, MIN receives direct retinal input and projects to various visual cortical areas. We examined the MIN of 15 normal adult cats with electrophysiological and anatomical techniques.
Oncostatin M and Transforming Growth Factor-β1 Induce Post-translational Modification and Hyaluronan Binding to CD44 in Lung-derived Epithelial Tumor Cells*

CD44, a receptor for hyaluronan (HA), has been implicated in tumor growth and metastasis. Most CD44-positive cells fail to exhibit constitutive HA receptor function but CD44-mediated HA binding on hematopoetic cells can be induced by antibody cross-linking of the receptor and by physiologic stimuli, including cytokines. We now demonstrate that oncostatin M (OSM) and transforming growth factor-β1, cytokines known to regulate the growth of tumor cells, stimulate HA binding in lung epithelial-derived tumor cells. In lung epithelial-derived tumor cells, cytokine-induced binding resulted from post-translational modification of the receptor. OSM-induced HA binding was associated with a reduction in N-linked carbohydrate content of CD44. In addition, OSM induced HA binding via a novel mechanism requiring sulfation of chondroitin sulfate chains linked to CD44. The mechanism underlying transforming growth factor-β1 induced HA binding was distinct from the effects of OSM. The data presented indicate that modulation of the glycosylation and sulfation of CD44 by cytokines provides mechanisms for regulating cell adhesion during tumor growth and metastasis.
Only one item left?: Heuristic Information Trumps Calorie Count When Supporting Healthy Snacking Under Low Self-Control

Pursuing the goal of a healthy diet may be challenging, especially when self-control resources are low. Yet many persuasive user interfaces fostering healthy choices are designed for situations with ample self-control, e.g. showing nutritional information to support reflective decision making. In this paper we propose that under low self-control, persuasive user interfaces need to rely on simple heuristic decision making to be successful. We report an experiment that tested this assumption in a 2 (low vs. high self-control) x 2 (calorie vs. heuristic information) design. The results reveal a significant interaction effect. Participants with low self-control resources chose the healthy snack more often when snacks were labelled with heuristic information than when they were labelled with calorie information. Both strategies were about equally successful for participants with high self-control. Exploiting situations of low self-control with heuristic information is a new and promising approach to designing persuasive technology for healthy eating.
Group nearest neighbor queries

Given two sets of points P and Q, a group nearest neighbor (GNN) query retrieves the point(s) of P with the smallest sum of distances to all points in Q. Consider, for instance, three users at locations q/sub 1/ q/sub 2/ and q/sub 3/ that want to find a meeting point (e.g., a restaurant); the corresponding query returns the data point p that minimizes the sum of Euclidean distances |pq/sub i/| for 1/spl les/i/spl les/3. Assuming that Q fits in memory and P is indexed by an R-tree, we propose several algorithms for finding the group nearest neighbors efficiently. As a second step, we extend our techniques for situations where Q cannot fit in memory, covering both indexed and nonindexed query points. An experimental evaluation identifies the best alternative based on the data and query properties.
Prevalence of Enterotoxigenic Staphylococcus aureus Isolated From Chicken Nugget in Iran

Background: The enterotoxigenic Staphylococcus aureus is considered as one of the most important cause of food poisoning that manifests with gastroenteritis, diarrhea, and vomiting. Its complications usually occur when bacterial virulence genes are produced. The most important virulence factors are cell-associated components, exoenzymes, exotoxins, enterotoxins, and enterotoxin-like toxins. Objectives: The present study aimed to study the presence of S. aureus and its virulence factors in chicken nuggets in Iran. Materials and Methods: Totally, 420 chicken nuggets from five brands were collected from Isfahan and Chaharmahal-va-Bakhtiari provinces, Iran. Samples were cultured and the positive results were studied using ELISA and PCR for detection of classical staphylococcal enterotoxins and sea-sej virulence genes, respectively. Results: Results showed that 27 (6.42%) of 420 samples were contaminated with S. aureus with bacteria concentration between 6.1 × 103 to 8.4 × 101/mL. Totally, 33.33% of isolates produced SEA, 4.16% SEB, 12.50% SEC, 8.33% SED, 12.50% SEA + SEC, and 12.50% SEA + SED. The most commonly detected genes were sea (25%), sea + seg (8.33%), sec (12.50%), sea + sed (12.50%), and sea + sec + sej (12.50%). Conclusions: S. aureus can easily contaminate the chicken nugget and this contamination is usually associated with significant presences of virulence genes. Consumption of these nuggets certainly is associated with gastrointestinal diseases. Therefore, some food safety and quality standards should be applied and performed in most of the Iranian food units to control growth of S. aureus and its virulence factors.
Mode of Ca2+ action on ciliary beat frequency in single ovine airway epithelial cells

1 We analysed the kinetics of coupling between cytoplasmic calcium ([Ca2+]i) and ciliary beat frequency (CBF) using simultaneous single cilium recording and single cell [Ca2+]i measurements from cultured ovine tracheal epithelial cells. 2 CBF and [Ca2+]i (indicated by fura‐2) were measured at rest and in response to activation of the G‐protein coupled M3 muscarinic receptor by 10 μM acetylcholine (ACh). 3 Fourier transform analysis of 3 s data segments of light intensity from phase‐contrast microscopy showed no significant delay between changes in [Ca2+]i and CBF during a 2 min exposure to ACh and subsequent washout. 4 CBF time resolution was improved by computing instantaneous beat frequency. This revealed that CBF lagged the rapid increase in [Ca2+]i in response to ACh with a delay of less than 1 beat cycle (143 ms at 7 Hz). When CBF was estimated by an improved Fourier method, this delay was observed to be 70 ± 30 ms (mean ± s.e.m.; n= 20 cilia). During the slower return to baseline, a lag of 8 ± 3.2 s was observed, indicative of hysteresis. 5 While calmodulin inhibitors (calmidazolium and W‐7; each n= 5) decreased baseline CBF by an average of 1.1 ± 0.1 Hz, they did not alter the kinetic relationship between [Ca2+]i and CBF. Similarly, phosphatase inhibitors (okadaic acid and cyclosporin A; each n= 5), changed neither baseline CBF nor the kinetic coupling between [Ca2+]i and CBF. 6 These data suggest that the timing of Ca2+ action on CBF in ovine airway epithelial cells, is unlikely to be determined by phosphorylation reactions involving calmodulin or kinase/phosphatase reactions. 7 A simple model for Ca2+ stimulation of CBF is presented. Fits of the model to the data suggest four or more Ca2+ ions bind cooperatively to speed up CBF.
Does Globalization Affect Growth ? Evidence from a new Index of Globalization

The paper presents an index of globalization covering its three main dimensions: economic integration, social integration, and political integration. Using panel data for 123 countries in 1970-2000 it is analyzed empirically whether the overall index of globalization as well as sub-indexes constructed to measure the single dimensions affect economic growth. As the results show, globalization indeed promotes growth. The dimensions most robustly related with growth refer to actual economic flows and restrictions in developed countries. Although less robustly, information flows also promote growth whereas political integration has no effect.
In UX We Trust: Investigation of Aesthetics and Usability of Driver-Vehicle Interfaces and Their Impact on the Perception of Automated Driving

In the evolution of technical systems, freedom from error and early adoption plays a major role for market success and to maintain competitiveness. In the case of automated driving, we see that faulty systems are put into operation and users trust these systems, often without any restrictions. Trust and use are often associated with users' experience of the driver-vehicle interfaces and interior design. In this work, we present the results of our investigations on factors that influence the perception of automated driving. In a simulator study, N=48 participants had to drive a SAE level 2 vehicle with either perfect or faulty driving function. As a secondary activity, participants had to solve tasks on an infotainment system with varying aesthetics and usability (2x2). Results reveal that the interaction of conditions significantly influences trust and UX of the vehicle system. Our conclusion is that all aspects of vehicle design cumulate to system and trust perception.