Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

Network analysis became a powerful tool giving new insights to the understanding of cellular behavior. Heat shock, the archetype of stress responses, is a well-characterized and simple model of cellular dynamics. S. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and stress response at the gene expression level have been well characterized. However, the analysis of the reorganization of the yeast interactome during stress has not been investigated yet. We calculated the changes of the interaction-weights of the yeast interactome from the changes of mRNA expression levels upon heat shock. The major finding of our study is that heat shock induced a significant decrease in both the overlaps and connections of yeast interactome modules. In agreement with this the weighted diameter of the yeast interactome had a 4.9-fold increase in heat shock. Several key proteins of the heat shock response became centers of heat shock-induced local communities, as well as bridges providing a residual connection of modules after heat shock. The observed changes resemble to a ‘stratus-cumulus’ type transition of the interactome structure, since the unstressed yeast interactome had a globally connected organization, similar to that of stratus clouds, whereas the heat shocked interactome had a multifocal organization, similar to that of cumulus clouds. Our results showed that heat shock induces a partial disintegration of the global organization of the yeast interactome. This change may be rather general occurring in many types of stresses. Moreover, other complex systems, such as single proteins, social networks and ecosystems may also decrease their inter-modular links, thus develop more compact modules, and display a partial disintegration of their global structure in the initial phase of crisis. Thus, our work may provide a model of a general, system-level adaptation mechanism to environmental changes.
Comparisons of Walleye Pollock, Theragra chalcogramma, Harvest to Steller Sea Lion, Eumetopias jubatus, Abundance in the Bering Sea

Steller sea lion, Eumetipias jubatus, counts made on rookeries in the Gulf of Alaska, Aleutian Islands, and the Bering Sea from 1976 to 1991 were compared to annual estimates of walleye pollock, Theragra Chalcogramma, harvest to examine possible relationships between Steller sea lion abundance and commercial pollock fishing. Comparisons were made between Steller sea lion counts and pollock fishery data from the same year and from 1 to 5 years prior. Two sets of study areas were used, one encompassing 60 nmi or 120 nmi blocks around six major rookeries and another with 13 sites defined by 20 nmi radius rings around major rookeries. Lacking accurate measures of local pollock biomass, harvest data were used as approximations of annual differences in pollock abundance. Following methods used in Loughlin and Merrick (1989), correlation coefficients were calculated using a linear model and tested for significance using a 2-tailed null hypothesis (=O.O5). However, since the data are probably not normally distributed, Kendall's coefficients of rank correlation were also calculated and tested for significance (=0.05). Using the parametric approach, some significant positive -correlations were obtained comparing sea lion counts to pollock harvests 1 to 5 years prior (2 in the first set of comparisons and 8 in the second). These may indicate circumstances where pollock abundance was adequate to sustain the fishery while sea
The Taxonomic Significance of Species That Have Only Been Observed Once: The Genus Gymnodinium (Dinoflagellata) as an Example

Taxonomists have been tasked with cataloguing and quantifying the Earth’s biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been observed at the time and place of their original description are referred to as oncers. Oncers are important to our current understanding of biodiversity. They may be validly described species that are members of a rare biosphere, or they may indicate endemism, or that these species are limited to very constrained niches. Alternatively, they may reflect that taxonomic practices are too poor to allow the organism to be re-identified or that the descriptions are unknown to other researchers. If the latter are true, our current tally of species will not be an accurate indication of what we know. In order to investigate this phenomenon and its potential causes, we examined the microbial eukaryote genus Gymnodinium. This genus contains 268 extant species, 103 (38%) of which have not been observed since their original description. We report traits of the original descriptions and interpret them in respect to the status of the species. We conclude that the majority of oncers were poorly described and their identity is ambiguous. As a result, we argue that the genus Gymnodinium contains only 234 identifiable species. Species that have been observed multiple times tend to have longer descriptions, written in English. The styles of individual authors have a major effect, with a few authors describing a disproportionate number of oncers. The information about the taxonomy of Gymnodinium that is available via the internet is incomplete, and reliance on it will not give access to all necessary knowledge. Six new names are presented – Gymnodinium campbelli for the homonymous name Gymnodinium translucens Campbell 1973, Gymnodinium antarcticum for the homonymous name Gymnodinium frigidum Balech 1965, Gymnodinium manchuriensis for the homonymous name Gymnodinium autumnale Skvortzov 1968, Gymnodinium christenum for the homonymous name Gymnodinium irregulare Christen 1959, Gymnodinium conkufferi for the homonymous name Gymnodinium irregulare Conrad & Kufferath 1954 and Gymnodinium chinensis for the homonymous name Gymnodinium frigidum Skvortzov 1968.
2015 Ieee International Conference on Big Data (big Data) Evaluating Different Distributed-cyber-infrastructure for Data and Compute Intensive Scientific Application

—Scientists are increasingly using the current state of the art big data analytic software (e.g., Hadoop, Giraph, etc.) for their data-intensive applications over HPC environment. However, understanding and designing the hardware environment that these data-and compute-intensive applications require for good performance is challenging. With this motivation, we evaluated the performance of big data software over three different distributed-cyber-infrastructures, including a traditional HPC-cluster called SuperMikeII, a regular data-center called SwatIII, and a novel MicroBrick-based hyperscale system called CeresII, using our own benchmark Parallel Genome Assembler (PGA). PGA is developed atop Hadoop and Giraph and serves as a good real-world example of a data-as well as compute-intensive workload. To evaluate the impact of both individual hardware components as well as overall organization, we changed the configuration of SwatIII in different ways. Comparing the individual impact of different hardware components (e.g., network, storage and memory) over different clusters, we observed 70% improvement in the Hadoop-workload and almost 35% improvement in the Giraph-workload in SwatIII over SuperMikeII by using SSD (thus, increasing the disk I/O rate) and scaling it up in terms of memory (which increases the caching). Then, we provide significant insight on efficient and cost-effective organization of these hardware components. Here, The MicroBrick-based CeresII prototype shows similar performance as SuperMikeII while giving more than 2-times improvement in performance/$ in the entire benchmark test.
Approximate Inference Algorithms for Hybrid Bayesian Networks with Discrete Constraints

In this paper, we consider Hybrid Mixed Networks (HMN) which are Hybrid Bayesian Networks that allow discrete deterministic information to be modeled explicitly in the form of constraints. We present two approximate inference algorithms for HMNs that integrate and adjust well known algorithmic principles such as Generalized Belief Propagation, Rao-Blackwellised Importance Sampling and Constraint Propagation to address the complexity of modeling and reasoning in HMNs. We demonstrate the performance of our approximate inference algorithms on randomly generated HMNs.
Molecular Weight Distribution and Removal Characteristics in Source Water of Ganjiang River

Raw water in the Nanchang district of Ganjiang River and water after conventional treatment were estimated by the method of the ultra filtration to find out its molecular weight distribution. According to the result, the molecular weight distribution of the raw water in Ganjiang River shows the trend which has the large edges and small middle part, that is to say; the organic matter mainly centralizes in a scope whose molecular weight are larger than 30ku and less than 1ku, the middle part occupies a relatively small proportion. In winter low-water season, there is little organic matter in the river and the small molecular of the organic matter plays a dominant role. In the season of high-water, the amount of organic matter increases, and while the small molecular of organic matter decreases and large molecular of organic matter becomes a large part. The popular water purifying process in Nan Chang city is just to mainly remove the large molecular in the organic matter, which leads to a bad result，the low efficiency of removing the small molecular.
Neuropsychological and information processing deficits following mild traumatic brain injury

Neuroradiological and neuropathological investigations have found evidence of diffuse brain damage in the frontal and temporal lobes, corpus callosum, and fornices in patients who have sustained a mild traumatic brain injury (TBI). However, neuropsychological assessments of these patients do not typically target many of the subtle information processing deficits that may arise from diffuse damage involving the frontotemporal regions of the brain as well as white matter pathology, including the corpus callosum. Consequently, we have a limited understanding of the deficits that may be attributable to temporary or permanent disruptions to these functional pathways. This study assessed a group of mild TBI patients (N = 40) and a matched control group (N = 40) on a number of standard neuropsychological tests of selective and sustained attention, verbal and non-verbal fluency, and verbal memory. In addition, reaction time (RT) tasks, requiring both the inter- and intra-hemispheric processing of visual and tactile information, were used to assess the functional integrity of the tracts that are likely to be affected by diffuse damage. In the 1st month after sustaining their injury, the mild TBI group demonstrated deficits in attention, non-verbal fluency, and verbal memory. They also demonstrated slower visual and tactile RTs, with the visual RTs of mild TBI patients being more affected by increased task difficulty and the need to transfer information across the corpus callosum, than did their matched controls. (JINS, 2004, 10, 286–297.)
Assessment of Physicochemical Properties of Rituximab Related to Its Immunomodulatory Activity

Rituximab is a chimeric monoclonal antibody employed for the treatment of CD20-positive B-cell non-Hodgkin's lymphoma, chronic lymphocytic leukemia, rheumatoid arthritis, granulomatosis with polyangiitis and microscopic polyangiitis. It binds specifically to the CD20 antigen expressed on pre-B and consequently on mature B-lymphocytes of both normal and malignant cells, inhibiting their proliferation through apoptosis, CDC, and ADCC mechanisms. The immunomodulatory activity of rituximab is closely related to critical quality attributes that characterize its chemical composition and spatial configuration, which determine the recognition of CD20 and the binding to receptors or factors involved in its effector functions, while regulating the potential immunogenic response. Herein, we present a physicochemical and biological characterization followed by a pharmacodynamics and immunogenicity study to demonstrate comparability between two products containing rituximab. The physicochemical and biological characterization revealed that both products fit within the same response intervals exhibiting the same degree of variability. With regard to clinical response, both products depleted CD20+ B-cells until posttreatment recovery and no meaningful differences were found in their pharmacodynamic profiles. The evaluation of anti-chimeric antibodies did not show differential immunogenicity among products. Overall, these data confirm that similarity of critical quality attributes results in a comparable immunomodulatory activity.
The Effect of Marital Status and Children on Savings and Portfolio Choice

This paper investigates the impact of demographic shocks on optimal decisions about saving, life insurance, and, most centrally, asset allocation. We analyze these choices within the framework of a life-cycle model that features exogenous changes in family composition, heterogeneity in lifetime income, and uninsurable fluctuations in earnings and medical costs. Our analysis indicates that marital-status transitions and children can have important effects on optimal household decisions. Widowhood induces sharp reductions in the portfolio shares in stock, and the impact is largest for women and individuals with children. Divorce causes men and women to reallocate their portfolios in different directions; men choose much riskier allocations, while women opt for safer ones. Children play a fundamental role in the optimal portfolio decisions. Men with children, for example, increase their shares in response to divorce by less than half as much as men without children. Comparing our simulation results with panel-data evidence on stockholding from the PSID and the HRS, we conclude that changes in marital status and children matter empirically as well, but not always in the ways that the model predicts. JEL classification: G11; G22; D91; E21; I10; J12
Fish consumption during the first year of life and development of allergic diseases during childhood

Background: Fish consumption during infancy has been regarded as a risk factor for allergic disease but later evidence suggests a protective role. However, methodological limitations in the studies make conclusions uncertain. The aim of this study was to assess the association between fish consumption during the first year of life and development of allergic diseases by age 4.
Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin

The transition from endosymbiont to organelle in eukaryotic cells involves the transfer of significant numbers of genes to the host genomes, a process known as endosymbiotic gene transfer (EGT). In the case of plastid organelles, EGTs have been shown to leave a footprint in the nuclear genome that can be indicative of ancient photosynthetic activity in present-day plastid-lacking organisms, or even hint at the existence of cryptic plastids. Here, we evaluated the impact of EGT on eukaryote genomes by reanalyzing the recently published EST dataset for Chromera velia, an interesting test case of a photosynthetic alga closely related to apicomplexan parasites. Previously, 513 genes were reported to originate from red and green algae in a 1:1 ratio. In contrast, by manually inspecting newly generated trees indicating putative algal ancestry, we recovered only 51 genes congruent with EGT, of which 23 and 9 were of red and green algal origin, respectively, whereas 19 were ambiguous regarding the algal provenance. Our approach also uncovered 109 genes that branched within a monocot angiosperm clade, most likely representing a contamination. We emphasize the lack of congruence and the subjectivity resulting from independent phylogenomic screens for EGT, which appear to call for extreme caution when drawing conclusions for major evolutionary events.
Sodium channel gating in clonal pituitary cells. The inactivation step is not voltage dependent

We have determined the time course of Na channel inactivation in clonal pituitary (GH3) cells by comparing records before and after the enzymatic removal of inactivation. The cells were subjected to whole- cell patch clamp, with papain included in the internal medium. Inactivation was slowly removed over the course of 10 min, making it possible to obtain control records before the enzyme acted. Papain caused a large (4-100x) increase in current magnitude for small depolarizations (near -40 mV), and a much smaller increase for large ones (approximately 1.5x at +40 mV). For technical reasons it was sometimes convenient to study outward INa recorded with no Na+ outside. The instantaneous I-V (IIV) curve in this condition was nonlinear before papain, and more nearly linear afterwards. The gNa-V curve after papain, obtained by dividing the INa-V curve by the IIV curve, was left- shifted by at least 20 mV and steepened. A spontaneous 5-10 mV left shift occurred in the absence of papain. The rate of the inactivation step was found to vary only slightly from -100 mV to +60 mV, based on the following evidence. (a) Before papain, inactivation rate saturated with voltage and was constant from +20 to +60 mV. (b) We activated the channels with a brief pulse, and studied the time course of the current on changing the voltage to a second, usually more negative level (Na+ present internally and externally). The time course of inactivation at each voltage was obtained by comparing control traces with those after inactivation was removed. When the 5-10-mV spontaneous shift was taken into account, inactivation rate changed by less than 10% from -100 to +60 mV. The data are considered in terms of existing models of the Na channel.
Visual outcome following chemotherapy for progressive optic pathway gliomas

Optic pathway gliomas (OPG) are relatively indolent tumors that may occur sporadically or in association with neurofibromatosis 1. Treatment is initiated only when a clear clinical or radiological deterioration is documented. Chemotherapy is the standard first line of treatment. Due to the indolent nature of this tumor, the most important challenge in OPG treatment is vision preservation.
Cognitive and Energy Harvesting-Based D2D Communication in Cellular Networks: Stochastic Geometry Modeling and Analysis

While cognitive radio enables spectrum-efficient wireless communication, radio frequency (RF) energy harvesting from ambient interference is an enabler for energy-efficient wireless communication. In this paper, we model and analyze cognitive and energy harvesting-based device-to-device (D2D) communication in cellular networks. The cognitive D2D transmitters harvest energy from ambient interference and use one of the channels allocated to cellular users (in uplink or downlink), which is referred to as the D2D channel, to communicate with the corresponding receivers. We investigate two spectrum access policies for cellular communication in the uplink or downlink, namely, random spectrum access (RSA) policy and prioritized spectrum access (PSA) policy. In RSA, any of the available channels including the channel used by the D2D transmitters can be selected randomly for cellular communication, while in PSA the D2D channel is used only when all of the other channels are occupied. A D2D transmitter can communicate successfully with its receiver only when it harvests enough energy to perform channel inversion toward the receiver, the D2D channel is free, and the signal-to-interference-plus-noise ratio (SINR) at the receiver is above the required threshold; otherwise, an outage occurs for the D2D communication. We use tools from stochastic geometry to evaluate the performance of the proposed communication system model with general path-loss exponent in terms of outage probability for D2D and cellular users. We show that energy harvesting can be a reliable alternative to power cognitive D2D transmitters while achieving acceptable performance. Under the same SINR outage requirements as for the non-cognitive case, cognitive channel access improves the outage probability for D2D users for both the spectrum access policies. When compared with the RSA policy, the PSA policy provides a better performance to the D2D users. Also, using an uplink channel provides improved performance to the D2D users in dense networks when compared to a downlink channel. For cellular users, the PSA policy provides almost the same outage performance as the RSA policy.
Effectiveness of a Dry-Land Resistance Training Program on Strength, Power, and Swimming Performance in Paralympic Swimmers

Abstract Dingley, AA, Pyne, DB, Youngson, J, and Burkett, B. Effectiveness of a dry-land resistance training program on strength, power, and swimming performance in paralympic swimmers. J Strength Cond Res 29(3): 619–626, 2015—This study evaluated the effectiveness of a dry-land resistance training program in Paralympic swimmers to increase swimming power and strength measures, and how these changes affect swimming performance. Seven elite-level Paralympic swimmers (1 man and 6 women; age: 19.4 ± 6.5 years; body mass: 57 ± 12 kg; height: 1.66 ± 0.21 m) performed a 6-week coach-prescribed strength training intervention program designed to improve power, flexibility, and postural control. Exercises targeted the main swimming movements: the start and turn, postural control in the water, and the pull and kick focusing on the gluteals, upper body, and trunk. Swimming-specific tests, involving a 50-m time trial, and timed dive starts were conducted at baseline and after the 6-week program. A bilateral swim-bench ergometer and jump tests were conducted to quantify arm and leg strength and power. After the 6-week intervention, 50-m time trials improved by 1.2%, ±1.5% (mean, ±90% confidence limits). Increases in both mean power (6.1%, ±5.9%) and acceleration (3.7%, ±3.7%) generated during the dive start enabled swimmers to substantially improve start times to the 5-m (5.5%, ±3.2) and 15-m (1.8%, ±1.1%) marks. The resistance training intervention resulted in a very large (r = 0.78, ±0.37) correlation between dive start velocity and the counter movement jump mean velocity. The 6-week resistance training program for Paralympic swimmers yielded substantial improvements in dry-land measures that corresponded with improvements in both timed dive starts and 50-m time trial performance, thus highlighting the usefulness of dry-land training for enhancing swimming performance in Paralympic swimming.