Miracle-dz/UniFAR-FTUs huggingface dataset:
maternally expressed gene1 Is a Novel Maize Endosperm Transfer Cell–Specific Gene with a Maternal Parent-of-Origin Pattern of Expression

Growth of the maize (Zea mays) endosperm is tightly regulated by maternal zygotic and sporophytic genes, some of which are subject to a parent-of-origin effect. We report here a novel gene, maternally expressed gene1 (meg1), which shows a maternal parent-of-origin expression pattern during early stages of endosperm development but biallelic expression at later stages. Interestingly, a stable reporter fusion containing the meg1 promoter exhibits a similar pattern of expression. meg1 is exclusively expressed in the basal transfer region of the endosperm. Further, we show that the putatively processed MEG1 protein is glycosylated and subsequently localized to the labyrinthine ingrowths of the transfer cell walls. Hence, the discovery of a parent-of-origin gene expressed solely in the basal transfer region opens the door to epigenetic mechanisms operating in the endosperm to regulate certain aspects of nutrient trafficking from the maternal tissue into the developing seed.
Recombinase and translesion DNA polymerase decrease the speed of replication fork progression during the DNA damage response in Escherichia coli cells

The SOS response is a DNA damage response pathway that serves as a general safeguard of genome integrity in bacteria. Extensive studies of the SOS response in Escherichia coli have contributed to establishing the key concepts of cellular responses to DNA damage. However, how the SOS response impacts on the dynamics of DNA replication fork movement remains unknown. We found that inducing the SOS response decreases the mean speed of individual replication forks by 30–50% in E. coli cells, leading to a 20–30% reduction in overall DNA synthesis. dinB and recA belong to a group of genes that are upregulated during the SOS response, and encode the highly conserved proteins DinB (also known as DNA polymerase IV) and RecA, which, respectively, specializes in translesion DNA synthesis and functions as the central recombination protein. Both genes were independently responsible for the SOS-dependent slowdown of replication fork progression. Furthermore, fork speed was reduced when each gene was ectopically expressed in SOS-uninduced cells to the levels at which they are expressed in SOS-induced cells. These results clearly indicate that the increased expression of dinB and recA performs a novel role in restraining the progression of an unperturbed replication fork during the SOS response.
A new interpretation of the ability of global models to simulate the MJO

Statistical diagnostics have led to a common perception that only few global models can reproduce the Madden‐Julian Oscillation (MJO). Here we demonstrate, using a method of tracking individual MJO events, that this perception is incorrect. Of 27 global model simulations diagnosed, all produced large‐scale slowly eastward propagating signals in precipitation, which are taken as manifestations of the MJO. The difference is some model produced them frequently, others infrequently. There is no statistically significant distinction between the strength and propagation speeds of MJO events produced by most of these models. A hypothesis is proposed to interpret our results: A model can produce the MJO only in a particular background state. If the background state of a model can be constantly in a condition that is conducive to its production of the MJO, this model simulates the MJO frequently. If not, this model can still produce the MJO but only infrequently when its seasonal background state occasionally migrates into a condition that is conducive to its production of the MJO. Preliminary results from testing this hypothesis are presented.
Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle

Most reductionist theories of muscle attribute a fiber's mechanical properties to the scaled behavior of a single half-sarcomere. Mathematical models of this type can explain many of the known mechanical properties of muscle but have to incorporate a passive mechanical component that becomes ∼300% stiffer in activating conditions to reproduce the force response elicited by stretching a fast mammalian muscle fiber. The available experimental data suggests that titin filaments, which are the mostly likely source of the passive component, become at most ∼30% stiffer in saturating Ca2+ solutions. The work described in this manuscript used computer modeling to test an alternative systems theory that attributes the stretch response of a mammalian fiber to the composite behavior of a collection of half-sarcomeres. The principal finding was that the stretch response of a chemically permeabilized rabbit psoas fiber could be reproduced with a framework consisting of 300 half-sarcomeres arranged in 6 parallel myofibrils without requiring titin filaments to stiffen in activating solutions. Ablation of inter-myofibrillar links in the computer simulations lowered isometric force values and lowered energy absorption during a stretch. This computed behavior mimics effects previously observed in experiments using muscles from desmin-deficient mice in which the connections between Z-disks in adjacent myofibrils are presumably compromised. The current simulations suggest that muscle fibers exhibit emergent properties that reflect interactions between half-sarcomeres and are not properties of a single half-sarcomere in isolation. It is therefore likely that full quantitative understanding of a fiber's mechanical properties requires detailed analysis of a complete fiber system and cannot be achieved by focusing solely on the properties of a single half-sarcomere.
Target-color learning and its detection for non-stationary scenes by nearest neighbor classification in the spatio-color space

We propose a method for detecting foreground objects in non-stationary scenes. The method can (1) detect arbitrary foreground objects without any prior knowledge of them, (2) identify background pixels under various changes in a background scene, and (3) detect minor difference between the background and target colors. Online detection is realized by the nearest neighbor classifier in the 5D xy-YUV space (the spatio-color space), consisting of the x and y coordinates of an image and Y, U, and V colors, which holds rectified training data of background colors and automatically learned target colors. We conducted experiments to confirm the effectiveness of our method.
Prevalence of mastitis pathogens in Ragusa, Sicily, from 2000 to 2006.

The objective of this study was to report the prevalence of intramammary infections (IMI) in Ragusa, Sicily, from milk samples (n = 18,711) collected between October 2000 and June 2006 from 101 dairy herds. Milk samples were collected at 9,747 cow sampling events from 5,285 individual cows. Samples were individual quarter (92.8%) or composite samples (7.2%) from an individual cow. Logistic regression was used to examine the prevalence of IMI at the level of milk sample and at the level of cow, controlling for year and season of collection, type of sample (individual quarter or composite), and type of housing and bedding of the cow at the time of collection. Bedding and housing types were as follows, respectively (number of herd groups): bedding: none (61), organic [51 (straw, 50; sawdust, 1)], and sand (3); housing: bedded pack (37), free stalls (57), tie stalls (4), and paddock (17). Raw prevalence of cow IMI for a sample event was as follows (percentage of cow samples): no growth, 47.4%; coagulase-negative staphylococci, 22.6%; Staphylococcus aureus, 20.6%; other Streptococcus spp. , 11.1%; Streptococcus agalactiae, 2.3%; coliform bacteria, 2.9%; and other organisms, 5.8%. Prevalence of IMI differed by bedding type for Staph. aureus (none, 24.5%; organic, 12.7%; sand, 12.3%) and coagulase-negative staphylococci (none, 13.1%; organic, 27.4%; sand, 26.9%) but not for Streptococcus spp. or coliform bacteria. Prevalence of Streptococcus spp. IMI differed by housing type (tie stalls, 22.2%; bedded pack, 12.8%; free stalls, 8.4%; paddock, 7.1%). Housing was not associated with the prevalence of IMI for other bacteria. Herd monthly prevalence of Staph. aureus and Streptococcus spp. IMI was associated with decreased mean milk production (Staph. aureus, -1.42 kg/d per cow, SEM 0.51; Streptococcus spp., -1.31 kg/d per cow, SEM 0.64) and increased mean linear score (Staph. aureus, 1.01 units/d per cow, SEM 0.16; Streptococcus spp., 0.59 units/d per cow, SEM 0.22). Herds (n = 11) with a mean linear score (MLS) less than 3.3 units had the lowest prevalence of Staph. aureus IMI and monthly MLS and the greatest monthly mean milk production compared with other herds grouped by MLS [MLS 3.31 to 3.99 (n = 20), MLS 4.00 to 4.46 (n = 20), MLS >4.46 (n = 17), and MLS not available (n = 33)]. Implementation of a milk quality program to control gram-positive organisms is important for Ragusa.
Towards wireless emotional valence detection from EEG

Intelligent affective computers can have many medical and non-medical applications. However today's affective computers are limited in scope by their transferability to other application environments or that they monitor only one aspect of physiological emotion expression. Here, the use of a wireless EEG system, which can be implemented in a body area network, is used to investigate the potential of monitoring emotional valence in EEG, for application in real-life situations. The results show 82% accuracy for automatic classification of positive, negative and neutral valence based on film clip viewing, using features containing information on both the frequency content of the EEG and how this changes over time.
Investigating Fruit and Vegetable Consumption Using the Transtheoretical Model

Purpose. Test the applicability of the transtheoretical model (TTM) to adult fruit/vegetable consumption. Design. Cross-sectional random-digit dial survey. Setting. Hawaii. Subjects. 700 (62.6% female; age [mean ± SD], 47 ± 17.1 years; education [mean ± SD], 14.6 ± 2.8 years; 35.0% white, 31.1% Asian, 22.1% native Hawaiian/Pacific Islander, 11.8% other). Measures. Stages, processes, self-efficacy, decisional balance, and self-reported fruit/vegetable consumption. Analysis. Confirmatory factor analysis tested the factor structure. Analyses of variance were used to explore stage differences in constructs. Results. Stage distribution was precontemplation (33%), contemplation (4%), preparation (37%), action (3%), and maintenance (23%). A 10-factor process model with two higher-order correlated factors (experiential and behavioral) provided the best data fit (X2 = 1446.12; df = 366; p < .0001; comparative fit index [CFI] = .89; standardized root mean square residual [SRMR] = .05). The self-efficacy structure fit the data well (X2 = 81.86; df = 9; p < .0001; CFI = .94; SRMR = .04), as did the decisional balance structure (X2 = 37.42; df = 19;p = .007; CFI = .99; SRMR = .02). Processes, self-efficacy, decisional balance, and fruit/vegetable consumption behavior differed significantly by stage, with medium effect sizes for most variables. Conclusion. The variables revealed adequate fit to the theorized measurement models. TTM predictions regarding stage differences in self-efficacy, pros and cons, and fruit/vegetable consumption were confirmed; however, most experiential and behavioral processes increased in the early stages and then leveled off.
Approximate value iteration for a class of deterministic optimal control problems with infinite state and input alphabets

We consider discrete-time deterministic optimal control problems in which termination at some finite, but not predetermined nor a-priori bounded time is mandatory. We characterize the value function as the maximal fixed point of a suitable dynamic programming operator and establish the convergence of both exact and approximate value iteration under very general assumptions, which cover the classical deterministic shortest path problem and its extension to hypergraphs as well as reachability and minimum-time problems for sampled versions of continuous control systems under constraints. In particular, the state and input alphabets are infinite sets or metric spaces, and the plant dynamics may be nonlinear and subject to disturbances and constraints. The optimization is in the minimax (or maximin) sense, the additive, extended real-valued running and terminal costs are undiscounted and may be unbounded and of arbitrary signs, the value function is typically discontinuous, and our results do apply to the maximization of non-negative rewards under hard constraints.
Neonatal outcome of 724 children born after ICSI using non-ejaculated sperm.

BACKGROUND Safety concerns have been expressed regarding the use of immature non-ejaculated spermatozoa for ICSI. Therefore, adverse health outcomes, birth parameters, major anomaly rates and chromosomal aberrations in children born after ICSI using testicular and epididymal sperm were investigated. METHODS Questionnaire data and results of physical examinations of 530 children born after ICSI with testicular sperm and of 194 children born after ICSI with epididymal sperm were compared with data on 2516 ICSI children born using ejaculated sperm. RESULTS Birth parameters, stillborn rates, prematurity rates and rates of low birthweight and very low birthweight were comparable between the non-ejaculated and the ejaculated sperm groups. The perinatal death rate was higher for twins but not for singletons in the non-ejaculated sperm group in comparison to the control cohort of children born using ejaculated sperm. A non-significant increase in major anomalies was reported in the non-ejaculated sperm group in comparison to the ejaculated sperm group. No more anomalies were observed in pre- and post-natal karyotypes from viable pregnancies established using non-ejaculated sperm versus ejaculated sperm. CONCLUSION Overall neonatal health in terms of birth parameters, major anomalies and chromosomal aberrations in our large cohort of children born by the use of non-ejaculated sperm seems reassuring in comparison to the outcome of children born after the use of ejaculated sperm.
The Power of Choice in Data-Aware Cluster Scheduling

Providing timely results in the face of rapid growth in data volumes has become important for analytical frameworks. For this reason, frameworks increasingly operate on only a subset of the input data. A key property of such sampling is that combinatorially many subsets of the input are present. We present KMN, a system that leverages these choices to perform data-aware scheduling, i.e., minimize time taken by tasks to read their inputs, for a DAG of tasks. KMN not only uses choices to co-locate tasks with their data but also percolates such combinatorial choices to downstream tasks in the DAG by launching a few additional tasks at every upstream stage. Evaluations using workloads from Facebook and Conviva on a 100-machine EC2 cluster show that KMN reduces average job duration by 81% using just 5% additional resources.
Gullies, a critical link in landscape soil loss: A case study in the subhumid highlands of Ethiopia

Land use changes in many landscapes result in gully formation, carving up agricultural land and playing a large role in filling up downstream reservoirs by connecting uplands with rivers. This includes the Ethiopian highlands. Our objective is to begin investigating the interaction of upland and gully erosion and to quantify the portion of eroded sediment originating from a gully to prioritize erosion control practices. For this purpose, a 5‐m deep valley bottom gully of the 13‐ha catchment in the Debre Mawi watershed in the subhumid Ethiopian highland near Lake Tana was selected. The upstream and downstream gully discharge and sediment concentrations were measured over a 2‐year period. The results show that the sediment concentration at the outlet was about 10 times greater than at the inlet. The sediment budget calculation showed that about over 90% of the sediment at the outlet originated from within the gully. Hysteresis analysis of the sediment concentration discharge relationship showed that sediment supply from the upland was limited, but sediment was always available to be eroded and transported in the gully because of bank failures and headcut retreat. Thus, to reduce sediment loads in rivers and consequent adverse downstream impacts, designing cost‐effective measures to treat gullies should be a priority in the subhumid Ethiopian highlands.
On the Use of Speech and Face Information for Identity Verification

{T}his report first provides a review of important concepts in the field of information fusion, followed by a review of important milestones in audio-visual person identification and verification. {S}everal recent adaptive and non-adaptive techniques for reaching the verification decision (i.e., to accept or reject the claimant), based on speech and face information, are then evaluated in clean and noisy audio conditions on a common database; it is shown that in clean conditions most of the non-adaptive approaches provide similar performance and in noisy conditions most exhibit a severe deterioration in performance; it is also shown that current adaptive approaches are either inadequate or utilize restrictive assumptions. A new category of classifiers is then introduced, where the decision boundary is fixed but constructed to take into account how the distributions of opinions are likely to change due to noisy conditions; compared to a previously proposed adaptive approach, the proposed classifiers do not make a direct assumption about the type of noise that causes the mismatch between training and testing conditions. {T}his report is an extended and revised version of {IDIAP-RR} 02-33.
Matrix singular value decomposition for pole-free solutions of homogeneous matrix equations as applied to numerical modeling methods

A general technique for solving homogeneous matrix equations as applied to numerical modeling procedures in microwave and millimeter-wave structures is introduced. By using singular value decomposition, well-known numerical problems related to poles and steep gradients in the determinant function are eliminated. The proposed technique is generally applicable, improves the accuracy and reliability of computed results, and significantly reduces the CPU time due to a more moderate behavior of the function to be analyzed. A dispersion characteristics example of a conductor-backed slotline MMIC structure illustrates the advantage of the pole-free formulation over conventional determinant calculations. <<ETX>>
Self-peptide released from class II HLA-DR1 exhibits a hydrophobic two- residue contact motif

Peptide fragments of foreign and self-proteins are of great immunologic importance as their binding to major histocompatibility complex (MHC) class I or II molecules makes an interaction with a corresponding T cell receptor possible. Recently, allele-specific peptide sequence motifs proved to be responsible for MHC binding, no matter whether self- or non-self-antigens were involved. Up to now, all investigated human class II-associated peptides were derived from foreign antigenic proteins. Therefore, we undertook sequence and binding analyses with a 16-mer self-peptide (SP3) that has been eluted from HLA-DR1. Here we demonstrate, by synthetic polyalanine-based 13-mer analogues of SP3, that two bulky hydrophobic anchor residues with relative spacing i, i + 8 are sufficient for high affinity binding. This is consistent with the hydrophobic i, i + 8 binding pattern recently found for DR-restricted T cell epitopes. Nevertheless, highly helical alanine-based design peptides with anchor spacing i, i + 9 exhibit maximal affinity, whereas replacement of alanine by helix destabilizing proline abrogates binding. Thus, a two-residue contact motif is the common minimal requirement of self- and foreign peptides for high affinity anchoring to HLA-DR1. In contrast to class I, the anchor spacing of DR1- associated peptides seems to bear some variability due to conformational diversity.
Three‐dimensional texture of natural pseudotachylyte: Pseudotachylyte formation mechanism in hydrous accretionary complex

Melt‐origin pseudotachylyte is the most reliable seismogenic fault rock. It is commonly believed that pseudotachylyte generation is rare in the plate subduction zone where interstitial fluids are abundant and can trigger dynamic fault‐weakening mechanisms such as thermal pressurization. Some recent studies, however, have discovered pseudotachylyte‐bearing faults in exhumed ancient accretionary complexes, indicating that frictional melting also occurrs during earthquakes in subduction zones. To clarify the pseudotachylyte generation mechanism and the variation of slip behavior in the plate subduction zone, a pseudotachylyte found in the exhumed fossil accretionary complex (the Shimanto Belt, Nobeoka, Japan) was re‐focused and microscopic and three‐dimensional observations of the pseudotachylyte‐bearing fault were performed based on optical, electron, and X‐ray microscope images. Based on the patterns contained in the fragment, the pseudotachylyte is divided into four domains, although no clear domain boundaries or layering structures are not found. Three‐dimensional observation also suggests that the pseudotachylyte were fragmented or isolated by cataclasite or carbonate breccia. The pseudotachylyte was rather injected into the surrounding carbonate breccia, which is composed of angular fragments of the host rock and a matrix of tiny crystalline carbonate. The pseudotachylyte volume was extracted from the X‐ray microscope image and the heat abundance consumed by the pseudotachylyte generation was estimated at 2.18 MJ/m2, which can be supplied during a slip of approximately 0.5 m. These observations and calculations, together with the results of the previous investigations, suggest hydrofracturing and rapid carbonate precipitation that preceded or accompanied the frictional melting. Dynamic hydrofracturing during a slip can be caused by rapid fluid pressurization, and can induce abrupt decrease in fluid pressure while drastically enhancing the shear strength of the shear zone. Consequently, frictional heating would be reactivated and generate the pseudotachylyte. These deformation processes can explain pseudotachylyte generation in hydrous faults with the impermeable wall rock.
Analysis and Synthesis of Robust Control Systems Using Linear Parameter Dependent Lyapunov Functions

This note provides sufficient robust stability conditions for continuous time polytopic systems. They are obtained from the Frobenius-Perron Theorem applied to the time derivative of a linear parameter dependent Lyapunov function and are expressed in terms of linear matrix inequalities (LMI). They contain as special cases, various sufficient stability conditions available in the literature to date. As a natural generalization, the determination of a guaranteed H2 cost is addressed. A new gain parametrization is introduced in order to make possible the state feedback robust control synthesis using parameter dependent Lyapunov functions through linear matrix inequalities. Numerical examples are included for illustration