Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model the relationship between genome-wide dynamics of chromatin marks and the local occurrence of computationally predicted TF binding sites. By applying this computational approach to a time course of Polycomb-mediated H3K27me3 marks during neuronal differentiation of murine stem cells, we identify several motifs that likely regulate the dynamics of this chromatin mark. Among these, the sites bound by REST and by the SNAIL family of TFs are predicted to transiently recruit H3K27me3 in neuronal progenitors. We validate these predictions experimentally and show that absence of REST indeed causes loss of H3K27me3 at target promoters in trans, specifically at the neuronal progenitor state. Moreover, using targeted transgenic insertion, we show that promoter fragments containing REST or SNAIL binding sites are sufficient to recruit H3K27me3 in cis, while deletion of these sites results in loss of H3K27me3. These findings illustrate that the occurrence of TF binding sites can determine chromatin dynamics. Local determination of Polycomb activity by REST and SNAIL motifs exemplifies such TF based regulation of chromatin. Furthermore, our results show that key TFs can be identified ab initio through computational modeling of epigenome data sets using a modeling approach that we make readily accessible.
The use of sticky ovitraps to estimate dispersal of Aedes aegypti in northeastern Mexico.

A newly designed sticky ovitrap was used to determine the dispersal flight of the dengue vector Aedes aegypti in northeastern Mexico. Unfed marked females were released in the field where 100 sticky ovitraps had been positioned within a circular area 300 m in diameter. Success of this method was represented by a 7.7% (31 of 401) recapture rate during a 19-day sampling period. The maximum dispersal distance was 120 m with a mean of 30.5 m +/- 4.5 SD. Drastic hot and dry climatic conditions at the study site may have restricted mosquito dispersal. As expected, mostly gravid female mosquitoes were captured in the ovitraps. The method of sticky ovitraps proved to be useful and inexpensive for Ae. aegypti dispersal studies in Latin American countries. In addition to the marked mosquito populations, unmarked Ae. aegypti, Culex sp. , roaches, and even small vertebrates such as lizards and sparrows were found glued to the sticky ovitraps. Based on these studies, the use of sticky ovitraps is recommended for Ae. aegypti dispersal studies, specially for dengue control programs in developing countries.
The giant low-density lipoproteins (LDL) accumulation in the multi-layer artery wall model

The mathematical, four-layer model of the LDL transport across the arterial wall including the sensitivity of the transport coefficients to the wall shear stress (WSS) is studied. In that model the advection-diffusion equations in porous media are used to determine the LDL concentration profiles in each layer of the arterial wall. We demonstrate the effect of the giant accumulation of the LDL in the intima layer. This property turns out to be an interplay between the layered structure of the arterial wall and WSS sensitivity of the endothelium. Interestingly, we also show that the single-layer models with the same WSS sensitivity mechanism and corresponding parameters, obscure the accumulation phenomenon, which predicts the one order of magnitude larger LDL concentration.
Robust single-view geometry and motion reconstruction

We present a framework and algorithms for robust geometry and motion reconstruction of complex deforming shapes. Our method makes use of a smooth template that provides a crude approximation of the scanned object and serves as a geometric and topological prior for reconstruction. Large-scale motion of the acquired object is recovered using a novel space-time adaptive, non-rigid registration method. Fine-scale details such as wrinkles and folds are synthesized with an efficient linear mesh deformation algorithm. Subsequent spatial and temporal filtering of detail coefficients allows transfer of persistent geometric detail to regions not observed by the scanner. We show how this two-scale process allows faithful recovery of small-scale shape and motion features leading to a high-quality reconstruction. We illustrate the robustness and generality of our algorithm on a variety of examples composed of different materials and exhibiting a large range of dynamic deformations.
Crystal structures of fibronectin-binding sites from Staphylococcus aureus FnBPA in complex with fibronectin domains

Staphylococcus aureus can adhere to and invade endothelial cells by binding to the human protein fibronectin (Fn). FnBPA and FnBPB, cell wall-attached proteins from S. aureus, have multiple, intrinsically disordered, high-affinity binding repeats (FnBRs) for Fn. Here, 30 years after the first report of S. aureus/Fn interactions, we present four crystal structures that together comprise the structures of two complete FnBRs, each in complex with four of the N-terminal modules of Fn. Each ≈40-residue FnBR forms antiparallel strands along the triple-stranded β-sheets of four sequential F1 modules (2–5F1) with each FnBR/2–5F1 interface burying a total surface area of ≈4,300 Å2. The structures reveal the roles of residues conserved between S. aureus and Streptococcus pyogenes FnBRs and show that there are few linker residues between FnBRs. The ability to form large intermolecular interfaces with relatively few residues has been proposed to be a feature of disordered proteins, and S. aureus/Fn interactions provide an unusual illustration of this efficiency.
Management of Onion Thrips [Thrips tabaci Lind. (Thysanoptera: Thripidae)] on Onion Using Eco-Friendly Cultural Practices and Varieties of Onion in Central Zone of Tigray, Ethiopia

Onion thrips, Thrips tabaci (Thysanoptera: Thripidae) is a major insect pest constraining onion production in the Central Zone of Tigray. Therefore, field experiment was conducted at Axum Agricultural Research from November 2015 to April 2016 to manage onion thrips using multiple techniques. The experiment was laid out in a randomized complete block design (RCBD) with split plot arrangement and replicated three times. Onion varieties Bombay Red and Nasik Red were used as main plot treatments and intercropping onion with one or two other vegetables including, cabbage, carrot and lettuce, as subplot treatments. Treating onion with the insecticide lambda-cyhalothrin (Karate) 5% EC and untreated sole onion were included as standard and control checks. Results showed that intercropping onion with cabbage, onion with cabbage + carrot and onion with cabbage + lettuce significantly reduced T. tabaci population by 58.47, 63.81 and 50.51%, respectively at higher infestations. Similarly, intercropping onion with cabbage, onion with cabbage + carrot and onion with lettuce + carrot showed a better effect in reducing thrips damage severity by 23.37, 23.09 and 17.66%, respectively, at higher infestations. Predatory thrips were observed on onion intercrops except the Karate 5% EC treated check. The highest marketable onion yield (35.52 t/ha) was obtained from onion intercropped with carrot and lettuce, though not significantly different from the untreated check. The lowest (23.54 t/ha) was obtained from onion intercropped with cabbage + lettuce. However, onion intercropped with lettuce gave the highest gross income (307344 ETB/ha). The lowest gross income was recorded from the insecticide treated plot (194583 ETB/ha). The study clearly showed that intercropping onion with other vegetables reduced the number of onion thrips and their damage on onion in the central zone of Tigray and hence can form an integral component in the integrated management of thrips on onion.
In vitro neurons in mammalian cortical layer 4 exhibit intrinsic oscillatory activity in the 10-to 50-Hz frequency range

We report here the presence of fast subthreshold oscillatory potentials recorded in vitro from neurons within layer 4 of the guinea pig frontal cortex. Two types of oscillatory neurons were recorded: (i) One type exhibited subthreshold oscillations whose frequency increased with membrane depolarization and encompassed a range of 10-45 Hz. Action potentials in this type of neuron demonstrated clear after-hyperpolarizations. (ii) The second type of neuron was characterized by narrow-frequency oscillations near 35-50 Hz. These oscillations often outlasted the initiating depolarizing stimulus. No calcium component could be identified in their action potential. In both types of cell the subthreshold oscillations were tetrodotoxin-sensitive, indicating that the depolarizing phase of the oscillation was generated by a voltage-dependent sodium conductance. The initial depolarizing phase was followed by a potassium conductance responsible for the falling phase of the oscillatory wave. In both types of cell, the subthreshold oscillation could trigger spikes at the oscillatory frequency, if the membrane was sufficiently depolarized. Combining intracellular recordings with Lucifer yellow staining showed that the narrow-frequency oscillatory activity was produced by a sparsely spinous interneuron located in layer 4 of the cortex. This neuron has extensive local axonal collaterals that ramify in layers 3 and 4 such that they may contribute to the columnar synchronization of activity in the 40- to 50-Hz range. Cortical activity in this frequency range has been proposed as the basis for the "conjunctive properties" of central nervous system networks.
Behaviour of free ranging wild boar towards their dead fellows: potential implications for the transmission of African swine fever

The behaviour of free ranging wild boar (Sus scrofa) towards carcasses of their conspecifics potentially infected with African swine fever (ASF) may significantly influence the course of an ASF epidemic. This study aims to better understand the behaviour of wild boar towards their dead fellows. Thirty-two wild boar carcasses on nine study sites in northeast Germany were monitored under field conditions by photo-trapping from October 2015 until October 2016. During this period, a total of 122 160 pictures were taken, thereof 16 111 pictures of wild boar. In both winter and summer, wild boar seemed to be particularly interested in the soil next to and underneath the carcasses. About one third of the visits of wild boar led to direct contact with dead conspecifics. The contacts consisted mostly in sniffing and poking on the carcass. Under the given ecological and climatic conditions, there was no evidence for intra-species scavenging. However, piglets were observed several times chewing bare bones once skeletonization of the carcasses was complete. It must be assumed that all these types of contact may represent a risk of transmission. Both the high tenacity of ASF virus and the long time wild boar carcasses can remain in the environment, allow the persistence of the virus for several months or even years. We therefore consider the rapid detection and removal (or destruction on the spot) of contaminated carcasses as an important control measure against ASF in wild boar.
Designing a dual page virtual keyboard for mental speller

Exploiting the novel human-machine interaction paradigm which is called brain-machine interface, we are dedicated to constructing a so called imitating-natural-reading visual evoked potential based mental speller for those with neuromuscular disorders and motor disabilities. These techniques also have potential applications in occasions such as navigating, diving and battlefield, etc. Users input a character to computer by gazing at the respective key of virtual keyboard on the screen. In order to realize the goal, we designed a virtual keyboard with double pages based on the past work. Analyzing the speed of communication of this paradigm reflect that it can boost up the bit rate significantly.
Possible dopaminergic stimulation of locus coeruleus α1‐adrenoceptors involved in behavioral activation

α1‐Adrenoceptors of the locus coeruleus (LC) have been implicated in behavioral activation in novel surroundings, but the endogenous agonist that activates these receptors has not been established. In addition to the canonical activation of α1‐receptors by norepinephrine (NE), there is evidence that dopamine (DA) may also activate certain brain α1‐receptors. This study examined the contribution of DA to exploratory activity in a novel cage by determining the effect of infusion of various dopaminergic and adrenergic drugs into the mouse LC. It was found that the D2/D3 agonist, quinpirole, which selectively blocks the release of CNS DA, produced a dose‐dependent and virtually complete abolition of exploration and all movement in the novel cage test. The quinpirole‐induced inactivity was significantly attenuated by coinfusion of DA but not by the D1 agonist, SKF38390. Furthermore, the DA attenuation of quinpirole inactivity was blocked by coinfusion of the α1‐adrenergic receptor antagonist, terazosin, but not by the D1 receptor antagonist, SCH23390. LC infusions of either quinpirole or terazosin also produced profound inactivity in DA‐β‐hydroxylase knockout (Dbh −/−) mice that lack NE, indicating that their behavioral effects were not due to an alteration of the release or action of LC NE. Measurement of endogenous DA, NE, and 5HT and their metabolites in the LC during exposure to the novel cage indicated an increase in the turnover of DA and NE but not 5HT. These results indicate that DA is a candidate as an endogenous agonist for behaviorally activating LC α1‐receptors and may play a role in the activation of this nucleus by novel surroundings. Synapse 62:516–523, 2008. © 2008 Wiley‐Liss, Inc.
Comparing Small‐ and Large‐Scale Models of Multicategory Buying Behavior

Focusing on the interdependence of product categories we analyze multicategory buying decisions of households by a finite mixture of multivariate Tobit-2 models with two response variables: purchase incidence and expenditure. Mixture components can be interpreted as household segments. Correlations for purchases of different categories turn out to be much more important than correlations among expenditures as well as correlations among purchases and expenditures of different categories. About 18% of all pairwise purchase correlations are significant. We compare the best-performing large-scale model with 28 categories to four small-scale models each with seven categories. In our empirical study the large-scale model clearly attains a better forecasting performance. The small-scale models provide several biased correlations and miss about 50% of the significant correlations which the large scale model detects. Copyright © 2013 John Wiley & Sons, Ltd.
Differential Spectrum of Kasami Power Permutations Over Odd Characteristic Finite Fields

Functions with low differential uniformity have important applications in cryptography, coding theory, and sequence design. The differential spectrum of a cryptographic function is of great interest for estimating its resistance to some variants of differential cryptanalysis. Finding power permutations (i.e., monomial bijective mappings) over finite fields with low differential uniformity and determining their differential spectra have received a lot of attention over the past two decades. The objective of this paper is to study the differential properties of the well-known Kasami power permutations <inline-formula> <tex-math notation="LaTeX">$x^{p^{2k}-p^{k}+1}$ </tex-math></inline-formula> over <inline-formula> <tex-math notation="LaTeX">$ {\mathrm {GF}}(p^{n})$ </tex-math></inline-formula>, where <inline-formula> <tex-math notation="LaTeX">$p$ </tex-math></inline-formula> is an odd prime and <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> is an integer with <inline-formula> <tex-math notation="LaTeX">$\gcd (n,k)=1$ </tex-math></inline-formula>. It turns out that this family of monomials is differentially <inline-formula> <tex-math notation="LaTeX">$(p+1)$ </tex-math></inline-formula>-uniform. Our result in the case of <inline-formula> <tex-math notation="LaTeX">$p=3$ </tex-math></inline-formula> gives an affirmative solution to a recent conjecture by Xu, Cao, and Xu. Most notably, the differential spectrum of this family of power permutations is completely determined.
Investigating the case of human nose shape and climate adaptation

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.
Is the Effect of Inguinal Field Block With 0.5% Bupivacaine on Postoperative Pain After Hernia Repair Enhanced by Addition of Ketorolac or S(+) Ketamine?

Objective: The aim of the study was to assess whether coadministration of S(+) ketamine or ketorolac would enhance or prolong local analgesic effect of bupivacaine after inguinal hernia repair. Design: Prospective double-blind randomized study evaluating pain intensity after surgery under general anesthesia. Setting: Outpatient facilities of the University Hospital of Lausanne. Patient: Thirty-six ASA I-II outpatients scheduled for elective day-case inguinal herniorraphy. Intervention: Analgesia strategy consisted of a wound infiltration and an inguinal field block either with 30 mL bupivacaine (0.5%) or with the same volume of a mixture of 27 mL bupivacaine (0.5%) + 3 mL S(+) ketamine (75 mg) or a 28 mL bupivacaine (0.5%) + 2 mL ketorolac (60 mg). Postoperative analgesic regimen was standardized. Outcome Measures: Pain intensity was assessed with a Visual Analog Scale, a verbal rating score, and by pressure algometry 2, 4, 6, 24, and 48 hours after surgery. Results: The 3 groups of patients experienced the highest Visual Analog Scale pain score at 24 hours, which was different from those at 6 and 48 hours (P < 0.05). Apart from a significantly lower pain sensation (verbal rating score) in the ketorolac group at 24 and 48 hours and only at 48 hours with ketamine, there were no other differences in pain scores, pain pressure thresholds, or rescue analgesic consumption between groups throughout the 48-hour study period. Conclusion: The addition of S (+)-ketamine or ketorolac only minimally improves the analgesic effect of bupivacaine. This may be related to the tension-free hernia repair technique associated with low postoperative pain.
The evaluation of deaths due to methyl alcohol intoxication

Background: Methanol poisoning is a serious medical, social and economic problem that may cause severe illness or death. After methanol ingestion, central nervous system depression, headache, dizziness, nausea, lack of coordination, and confusion begins. Once the initial symptoms have passed, a second set of symptoms arises, 10 to 30 hours after the initial exposure to methanol, including blurring or complete loss of vision and acidosis. Methanol poisoning by ingestion is a world-wide problem, and in some regions it is connected with high morbidity and mortality. The lethal dose of methanol in humans shows pronounced individual differences ranging from 15 to 500 ml. Methods: The records of the First Specialization Board of the Council of Forensic Medicine between 2002 and 2010 were reviewed retrospectively for all methyl alcohol poisoning cases. Results: There were 383 cases recorded. 360 (94%) of total fatalities were men and 23 (6%) were women. The age range was between 17 and 89. Although patients were conscious, cooperative, oriented at first, deteriorated general health state, metabolic acidosis and neurologic sequelae with severe electrocardiographic (ECG) changes were seen in progress of time. The laboratory findings and MRI imaging method were applied to assess progress and medical treatment. Unfortunately severe acidosis, central nervous system (CNS) sequelae and a lethal outcome occurred. The methyl alcohol blood concentrations ranged from 0 to 826 mg per 100 ml. The most common macroscopic and microscopic finding was lung edema, cerebral and cerebellar hemorrhage, ischemic changes in the brain and optic neuritis. Putaminal necrosis and hemorrhage, brainstem petechial hemorrhage, myocardial acute ischemic changes, thalamic and hypothalamic hemorrhage were detected rarely. Conclusions: This is the first study to report postmortem findings, clinical reports, crime scene reports and eye witness accounts to investigate methyl alcohol poisoning cases from medico-legal point of view in Turkey. Methanol poisoning by ingestion is a world-wide problem with high morbidity and mortality. For preventing methanol deaths, both awareness and public education must be increased.