Miracle-dz/UniFAR-FTUs huggingface dataset:
Yeast Two-Hybrid Systems and Protein Interaction Mapping Projects for Yeast and Worm

The availability of complete genome sequences necessitates the development of standardized functional assays to analyse the tens of thousands of predicted gene products in high‐throughput experimental settings. Such approaches are collectively referred to as ‘functional genomics’. One approach to investigate the properties of a proteome of interest is by systematic analysis of protein–protein interactions. So far, the yeast two‐hybrid system is the most commonly used method for large‐scale, high‐throughput identification of potential protein–protein interactions. Here, we discuss several technical features of variants of the two‐hybrid systems in light of data recently obtained from different protein interaction mapping projects for the budding yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Copyright © 2000 John Wiley & Sons, Ltd.
Some important consequences of lithospheric extension

Summary This paper briefly summarizes two of the important by-products of lithospheric extension during rifting. These are partial melting and the segregation and migration of basaltic melt to crustal levels, and the dynamical consequences of viscous flow in the lower lithosphere and asthenosphere. In both cases, the rift-stage subsidence may be significantly different from that predicted by a simple stretching model and may allow relative uplift of the rift zone, as well as subsidence. The dynamical model also predicts significant uplift of the rift shoulders, doming over the entire rift zone, and asymmetrical continental breakup at rifted continental margins. The relative importance of these predictions depends on the thermal and mechanical properties of the lithosphere. The model predictions help explain some of the discrepancies between the observed behaviour of rifts and results obtained from the simple stretching models.
Choosing the right resolution for vessel visualization in MR angiography

In magnetic resonance imaging (MRI), the theoretically achievable spatial resolution is characterized by the extent of k-space used for image reconstruction, which is inversely proportional to the pixel size. Therefore, spatial resolution increases with the extent of k-space sampled. Whereas the visible resolution is characterized by the object size at which the object of interest is visually separable from the background. Since noise in MRI data is "white" (uniformly distributed across the k-space), sampling more k-space results in adding more noise to the image. This can result in the decrease of the object visibility with increase in the spatial resolution. Hence, it is important to choose the right spatial resolution to view the object of interest. In this paper, we present a theoretical relationship between the visibility of vessel detail in magnetic resonance angiography (MRA) and also the probability of projection of vessels in the minimum intensity projection (MinIP) and maximum intensity projection (MIP) images as a function of spatial resolution. This theory lays a foundation for determining the extent of k-space that should be used for image reconstruction to visually identify a particular vessel/anatomic detail of interest. The theory is validated using imaging studies and it is demonstrated that the vessel information displayed in MRA as well as projection images can be maximized for a particular anatomic detail of interest by optimal choice of spatial resolution.
The Calcineurin-Dynamin 1 Complex as a Calcium Sensor for Synaptic Vesicle Endocytosis*

Exocytosis of synaptic vesicles is calcium-dependent, with synaptotagmin serving as the calcium sensor. Endocytosis of synaptic vesicles has also been postulated as a calcium-dependent process; however, an endocytic calcium sensor has not been found. We now report a physical association between the calcium-dependent phosphatase calcineurin and dynamin 1, a component of the synaptic endocytic machinery. The calcineurin-dynamin 1 interaction is calcium-dependent, with an EC50 for calcium in the range of 0.1–0.4 μm. Disruption of the calcineurin-dynamin 1 interaction inhibits clathrin-mediated endocytosis. Thus, the calcium-dependent formation of the calcineurin-dynamin 1 complex, delivered to the other endocytic coat proteins, provides a calcium-sensing mechanism that facilitates endocytosis.
SPASTICITY DUE TO PHENYTOIN TOXICITY

A young epileptic presented with spasticity as well as ataxia, diplopia and nystagmus; his serum phenytoin level was very high. All the abnormal signs disappeared after withdrawal of phenytoin. Spasticity, hyperreflexia, and clonus are features of phenytoin intoxication, present in this case, which are not commonly seen, and which have rarely been mentioned previously in the literature.
Nonminimum-phase FIR channel estimation using cumulant matrix pencils

This paper studies the blind estimation of single-input-single-output channels with finite impulse response (FIR) and nonminimum phase. Based on higher order statistics, we introduce a new algorithm that exploits a matrix pencil constructed from a set of cumulant matrices. By solving a generalized eigenvalue problem, channel estimates (up to a scalar ambiguity) can be obtained from nontrivial generalized eigenvectors of this cumulant matrix pencil. With multiple estimation results available, different schemes are given to extract channel information effectively. The proposed algorithm does not require exact knowledge of the channel length and can function properly under channel length overestimation. Numerical simulations demonstrate the robustness of this new algorithm to various adverse conditions.
Paleomagnetic Investigation of the Bonneville Alloformation, Lake Bonneville, Utah

Paleomagnetic secular variation in a portion of the Bonneville Alloformation is compared with secular variation in lacustrine sediments in the Mono Basin, California, and with secular variation in Lake Lahontan sediments in the northwestern Great Basin. The comparison places an age of about 18,000 yr B.P., and a span of 1000 to 3000 yr, on part of a transgressive stage of Lake Bonneville near Delta, Utah, that is coeval with a wet period in the Lahontan Basin.
Laboratory Validation of Inertial Body Sensors to Detect Cigarette Smoking Arm Movements

Cigarette smoking remains the leading cause of preventable death in the United States. Traditional in-clinic cessation interventions may fail to intervene and interrupt the rapid progression to relapse that typically occurs following a quit attempt. The ability to detect actual smoking behavior in real-time is a measurement challenge for health behavior research and intervention. The successful detection of real-time smoking through mobile health (mHealth) methodology has substantial implications for developing highly efficacious treatment interventions. The current study was aimed at further developing and testing the ability of inertial sensors to detect cigarette smoking arm movements among smokers. The current study involved four smokers who smoked six cigarettes each in a laboratory-based assessment. Participants were outfitted with four inertial body movement sensors on the arms, which were used to detect smoking events at two levels: the puff level and the cigarette level. Two different algorithms (Support Vector Machines (SVM) and Edge-Detection based learning) were trained to detect the features of arm movement sequences transmitted by the sensors that corresponded with each level. The results showed that performance of the SVM algorithm at the cigarette level exceeded detection at the individual puff level, with low rates of false positive puff detection. The current study is the second in a line of programmatic research demonstrating the proof-of-concept for sensor-based tracking of smoking, based on movements of the arm and wrist. This study demonstrates efficacy in a real-world clinical inpatient setting and is the first to provide a detection rate against direct observation, enabling calculation of true and false positive rates. The study results indicate that the approach performs very well with some participants, whereas some challenges remain with participants who generate more frequent non-smoking movements near the face. Future work may allow for tracking smoking in real-world environments, which would facilitate developing more effective, just-in-time smoking cessation interventions.
Microscopic conduction in cultured strands of neonatal rat heart cells measured with voltage-sensitive dyes.

Microscopic discontinuities in electrical activation were assessed in synthetic strands of neonatal rat myocytes cultured on a growth-directing matrix. An optical method using voltage-sensitive dye (RH-237) and a photodiode technique was used for recordings of membrane potential changes with subcellular resolution. Spatial resolution of the method (diameter of measurement area, 5.5 microns; interdiode distance, 30 microns) allowed for simultaneous measurements of cytoplasmic conduction time within a single cell and junctional conduction time across the cell border. In one-dimensional cell chains, where cells were juxtaposed by end-to-end connections but devoid of lateral connections, propagation of the excitation wave was strongly nonuniform: cytoplasmic conduction time was 38 +/- 30 (mean +/- SD) microseconds (n = 37), whereas junctional conduction time was 118 +/- 40 microseconds (n = 27, P < .0001). A mean delay introduced by a single junction was 80 microseconds, or 51% of conduction time. In two-dimensional strands consisting of several cells in width, which exhibited lateral as well as end-to-end connections, inhomogeneity of conduction was smaller: the cytoplasmic and junctional conduction times were 57 +/- 30 (n = 46) and 89 +/- 40 (n = 48) microseconds, respectively (P < .0001); mean junctional conduction delay was 32 microseconds (22% of conduction time). Mathematical modeling suggested that the averaging effect of lateral connections is caused by lateral convergence of local excitatory current beyond and lateral divergence before end-to-end connections. Our results demonstrate that the current flow through lateral cell-to-cell connections smooth the excitation wave front during longitudinal conduction in myocardial tissue.
Reprojection error based annealed particle filter for human upper body pose reconstruction

3D human pose reconstruction is a key concern in computer vision area in recent years. Due to the deficiency of depth information, reconstructing human pose from a single image or image sequences is still a difficult and challenging task. In this paper, we present an annealed particle filter algorithm based on reprojection error to recover the 3D configuration of human upper body, with the annotated joints' position in the image. In addition, we make simplifications to the weak perspective projection, and the 7 camera parameters to be estimated are reduced to only 1. Experiments show that our method is simple but exactly suitable for recovering articulated human upper body pose.
Developing a Flexible System-Modeling Environment for Engineers

We are developing a module-oriented, multiphysics, mixed fidelity system simulation environment that will enable engineers to rapidly analyze the performance of a system and to optimize its design. In the environment, physical components of the system are represented by software components, and are linked by ports that transfer and transform data between them. The model fidelity in a composite module may be specified independently, eg, one composite module may have a parametric model and another may have a three-dimensional finite-element model. In a prototype of the environment users can specify thermal radiation models for each system component, embed electrical circuits in each component, and set the external conditions for the system. During the simulation users can monitor the thermal and electrical behavior of the system. The latest software design for the environment promises greater flexibility in extending the environment for analyzing and optimizing a variety of complex systems.
Improving the evaluation of hydrological multi-model forecast performance in the Upper Danube Catchment

Medium range flood forecasting activities, driven by various meteorological forecasts ranging from high resolution deterministic forecasts to low spatial resolution ensemble prediction systems, share a major challenge in the appropriateness and design of performance measures. In this paper possible limitations of some traditional hydrological and meteorological prediction quality and verification measures are identified. Some simple modifications are applied in order to circumvent the problem of the autocorrelation dominating river discharge time-series and in order to create a benchmark model enabling the decision makers to evaluate the forecast quality and the model quality. Although the performance period is quite short the advantage of a simple cost-loss function as a measure of forecast quality can be demonstrated.
Structural Analysis of Determinants of Histo-Blood Group Antigen Binding Specificity in Genogroup I Noroviruses

ABSTRACT Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Susceptibility to the majority of NoV infections is determined by genetically controlled secretor-dependent expression of histo-blood group antigens (HBGAs), which are also critical for NoV attachment to host cells. Human NoVs are classified into two major genogroups (genogroup I [GI] and GII), with each genogroup further divided into several genotypes. GII NoVs are more prevalent and exhibit periodic emergence of new variants, suggested to be driven by altered HBGA binding specificities and antigenic drift. Recent epidemiological studies show increased activity among GI NoVs, with some members showing the ability to bind nonsecretor HBGAs. NoVs bind HBGAs through the protruding (P) domain of the major capsid protein VP1. GI NoVs, similar to GII, exhibit significant sequence variations in the P domain; it is unclear how these variations affect HBGA binding specificities. To understand the determinants of possible strain-specific HBGA binding among GI NoVs, we determined the structure of the P domain of a GI.7 clinical isolate and compared it to the previously determined P domain structures of GI.1 and GI.2 strains. Our crystallographic studies revealed significant structural differences, particularly in the loop regions of the GI.7 P domain, altering its surface topography and electrostatic landscape and potentially indicating antigenic variation. The GI.7 strain bound to H- and A-type, Lewis secretor, and Lewis nonsecretor families of HBGAs, allowing us to further elucidate the structural determinants of nonsecretor HBGA binding among GI NoVs and to infer several contrasting and generalizable features of HBGA binding in the GI NoVs. IMPORTANCE Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Recent epidemiological studies have shown increased prevalence of genogroup I (GI) NoVs. Although secretor-positive status is strongly correlated with NoV infection, cases of NoV infection associated with secretor-negative individuals are reported. Biochemical studies have shown that GI NoVs exhibit genotype-dependent binding to nonsecretor histo-blood group antigens (HBGAs). From our crystallographic studies of a GI.7 NoV, in comparison with previous studies on GI.1 and GI.2 NoVs, we show that genotypic differences translate to extensive structural changes in the loop regions that significantly alter the surface topography and electrostatic landscape of the P domain; these features may be indicative of antigenic variations contributing to serotypic differentiation in GI NoVs and also differential modulation of the HBGA binding characteristics. A significant finding is that the threshold length and the structure of one of the loops are critical determinants in the binding of GI NoVs to nonsecretor HBGAs.
Whole-grain, bran, and cereal fiber intakes and markers of systemic inflammation in diabetic women.

OBJECTIVE To evaluate the dietary predictors for the markers of systemic inflammation and endothelial dysfunction in patients with type 2 diabetes. RESEARCH DESIGN AND METHODS We examined whether intakes of whole grains and dietary fiber were associated with inflammatory indicators among 902 diabetic women in the Nurses' Health Study. RESULTS After adjustment for age, BMI, lifestyle, and dietary covariates, intakes of whole grains and bran were both associated with significantly decreasing trends of C-reactive protein (CRP) (P for trend = 0.03 and 0.007, respectively) and tumor necrosis factor-alpha receptor 2 (TNF-R2) (P for trend = 0.017 and 0.06). High intake of cereal fiber was also inversely associated with the lower levels of CRP (P for trend = 0.03) and TNF-R2 (P for trend = 0.01). The concentrations of CRP and TNF-R2 were 18 and 8% lower in the highest quintile of cereal fiber as compared with the lowest quintile. Dietary glycemic index was positively associated with CRP (P for trend = 0.04) and TNF-R2 (P for trend = 0.0008) levels. The concentrations of CRP and TNF-R2 were 32 and 11% higher, respectively, in the highest quintile of dietary glycemic index as compared with the lowest quintile. CONCLUSIONS Our data indicate that whole grains and a low-glycemic index diet may reduce systemic inflammation among women with type 2 diabetes.
Dietary restriction enhances neurotrophin expression and neurogenesis in the hippocampus of adult mice

The adult brain contains small populations of neural precursor cells (NPC) that can give rise to new neurons and glia, and may play important roles in learning and memory, and recovery from injury. Growth factors can influence the proliferation, differentiation and survival of NPC, and may mediate responses of NPC to injury and environmental stimuli such as enriched environments and physical activity. We now report that neurotrophin expression and neurogenesis can be modified by a change in diet. When adult mice are maintained on a dietary restriction (DR) feeding regimen, numbers of newly generated cells in the dentate gyrus of the hippocampus are increased, apparently as the result of increased cell survival. The new cells exhibit phenotypes of neurons and astrocytes. Levels of expression of brain‐derived neurotrophic factor (BDNF) and neurotrophin‐3 (NT‐3) are increased by DR, while levels of expression of high‐affinity receptors for these neurotrophins (trkB and trkC) are unchanged. In addition, DR increases the ratio of full‐length trkB to truncated trkB in the hippocampus. The ability of a change in diet to stimulate neurotrophin expression and enhance neurogenesis has important implications for dietary modification of neuroplasticity and responses of the brain to injury and disease.
Technical Development of a New Meningococcal Conjugate Vaccine

Background. Group A Neisseria meningitidis has been a major cause of bacterial meningitis in the sub-Saharan region of Africa in the meningitis belt. Neisseria meningitidis is an encapsulated pathogen, and antibodies against the capsular polysaccharide are protective. Polysaccharide–protein conjugate vaccines have proven to be highly effective against several different encapsulated bacterial pathogens. Purified polysaccharide vaccines have been used to control group A meningococcal (MenA) epidemics with minimal success. Methods. A monovalent MenA polysaccharide–tetanus toxoid conjugate was therefore developed. This vaccine was developed by scientists working with the Meningitis Vaccine Project, a partnership between PATH and the World Health Organization. Results. A high-efficiency conjugation method was developed in the Laboratory of Bacterial Polysaccharides in the Center for Biologics Evaluation and Research and transferred to the Serum Institute of India, Ltd, which then developed methods for purification of the group A polysaccharide and used its tetanus toxoid as the carrier protein to produce the now-licensed, highly effective MenAfriVac conjugate vaccine. Conclusions. Although many years of application of meningococcal polysaccharide vaccines have had minimal success in preventing meningococcal epidemics in the meningitis belt of Africa, our collaborative efforts to develop a MenA conjugate vaccine yielded a safe and highly effective vaccine.
Natural Conception May Be an Acceptable Option in HIV-Serodiscordant Couples in Resource Limited Settings

Many HIV serodiscordant couples have a strong desire to have their own biological children. Natural conception may be the only choice in some resource limited settings but data about natural conception is limited. Here, we reported our findings of natural conception in HIV serodiscordant couples. Between January 2008 and June 2014, we retrospectively collected data on 91 HIV serodiscordant couples presenting to Beijing Youan Hospital with childbearing desires. HIV counseling, effective ART on HIV infected partners, pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP) in negative female partners and timed intercourse were used to maximally reduce the risk of HIV transmission. Of the 91 HIV serodiscordant couples, 43 were positive in male partners and 48 were positive in female partners. There were 196 unprotected vaginal intercourses, 100 natural conception and 97 newborns. There were no cases of HIV seroconversion in uninfected sexual partners. Natural conception may be an acceptable option in HIV-serodiscordant couples in resource limited settings if HIV-positive individuals have undetectable viremia on HAART, combined with HIV counseling, PrEP, PEP and timed intercourse.
An age constraint on Gulf of California rifting from the Santa Rosalía basin, Baja California Sur, Mexico

Marine rocks of the Santa Rosalia basin, Baja California Sur, were sampled in a pilot study to determine their suitability for magnetostratigraphy and geochronology with the goal of providing an age constraint on Gulf of California rifting. Progressive demagnetization of samples from the Boleo Formation, the earliest marine sequence overlying the deeply eroded basement, reveals a high-coercivity characteristic remanent magnetization (ChRM) in addition to a low-coercivity overprint. The ChRM appears to be a primary magnetic remanence with stratigraphically bound normal- and reversed-polarity directions. A single ^(40)Ar/^(39)Ar isotopic age of 6.76 ± 0.90 Ma (2σ) was obtained for the cinta colorada, a tephra deposit of reversed paleomagnetic polarity within the Boleo Formation. The age of the cinta colorada is refined by calculating isotopic age probabilities for each of the reversed-polarity intervals of the geomagnetic polarity time scale (GPTS) in the ±2σ range 5.86–7.66 Ma. The interval with the highest probability is 6.57–6.94 Ma. In conjunction with the isotopic age, preliminary magnetostratigraphy of the Boleo Formation is correlated with the GPTS in order to further delineate the onset of marine sedimentation. The most likely correlation yields an age of 6.93–7.09 Ma (GPTS subchron C3Bn) for the base of the Boleo Formation and 6.14–6.27 Ma for the top. This correlation, indicating an average sedimentation rate of 28 ± 4 cm/k.y. , could be significantly altered if a more thorough magnetostratigraphy proved the existence of additional polarity intervals in the Boleo Formation. However, even if the isotopic age of the cinta colorada is used as the only age constraint, the result is consistent with data from the northern Gulf of California and shows that rifting started much earlier than the ca. 3.6 Ma commencement of sea-floor spreading at the mouth of the Gulf of California. The deposition of the Boleo Formation was probably related to an early phase of gulf rifting caused by a change in Pacific–North American plate motions.