Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of cki-2 during development in C. elegans

Rapid progress has been made toward understanding the significance of CDK inhibitor proteins (CKIs) in the regulation of cell cycle progression. The overall goal of this study has been targeted to further expand our knowledge of CKI function through the investigation of a previously uncharacterized CKI named cki-2 during development in C. elegans. The characterization of cki-2 using a reverse genetic approach called co-suppression has revealed a novel mechanism that cki-2 and its related cell cycle regulators are required for the appropriate elimination of centrioles during oogenesis. Loss of cki-2 in the germ line caused perdurance of centrioles into the one-cell embryo, resulting in supernumerary centrosomes and aberrant cell divisions in the first cell cycle. This was significantly suppressed by reduction of cyclin E and a Cdk2 homologue, indicating that these cell cycle regulators are involved in this critical developmental process. In order to further understand the function of cki-2, a yeast two-hybrid screen was conducted which allowed us to identify three CKI-2 interacting proteins: orthologues of PCNA (PCN-1), SUMO (SMO-1), and a RING finger protein called RNF-1. CKI-2 has functionally separable domains in its amino (Cyclin/Cdk binding)- and carboxy (PCNA binding)-terminus and they exert distinct roles in cell cycle progression. It was observed that CKI-2 is covalently modified by SUMO on its N-terminus and this causes CKI-2 to relocalize to thr nucleolus, which is associated with its rapid degradation. Since many RING finger proteins act as components of the multi-subunit E3 ubquitin ligases, we speculated that RNF-1 might be involved in the CKI-2 degradation. This possibility was tested by co-expression of RNF-1 with CKI-2, revealing that co-expression of RNF-1 suppresses the embryonic lethality caused by the CKI-2 overexpression and moreover, this is correlated with an increased rate of CKI-2 degradation. In addition, western blot analyses performed on different genetic backgrounds suggested that the CKI-2 degradation occurs in an ubiquitin-dependent manner through the proteasome-mediated proteolysis pathway. Furthermore, a yeast-based assay developed to test a possible role of SUMO in modulating the CKI-2/RNF-1 interaction demonstrated that SUMO may antagonize the interaction between CKI-2 and RNF-l, these highlighting an intriguing model that appropriate levels of CKI-2 are regulated through ubiquitin-dependent proteolysis mediated by RNF-l, and which maybe modulated by SUMO.
Connectionism and Cognitive Linguistics

Cognitive linguists hypothesize that language is the product of general cognitive abilities. Semantic and functional motivations are sought for grammatical patterns, sentence meaning is viewed as the result of constraint satisfaction, and highly regular linguistic patterns are thought to be mediated by the same processes as irregular patterns. In this paper, recent cognitive linguistics arguments emphasizing the schematicity continuum, the non-autonomy of syntax, and the non-compositionality of semantics are presented and their amenability to connectionist modeling described. Some of the conceptual matches between cognitive linguistics and connectionism are then illustrated by a back-propagation model of the diverse meanings of the preposition over. The pattern set consisted of a distribution of form-meaning pairs that was meant to be evocative of English usage in that the regularities implicit in the distribution spanned the spectrum from rules to partial regularities to exceptions. Under pressure to enc.
Rapid microsphere-assisted peptide screening (MAPS) of promiscuous MHCII-binding peptides in Zika virus envelope protein.

Despite promising developments in computational tools, peptide-class II MHC (MHCII) binding predictors continue to lag behind their peptide-class I MHC counterparts. Consequently, peptide-MHCII binding is often evaluated experimentally using competitive binding assays, which tend to sacrifice throughput for quantitative binding detail. Here, we developed a high-throughput semiquantitative peptide-MHCII screening strategy termed microsphere-assisted peptide screening (MAPS) that aims to balance the accuracy of competitive binding assays with the throughput of computational tools. Using MAPS, we screened a peptide library from Zika virus envelope (E) protein for binding to four common MHCII alleles (DR1, DR4, DR7, DR15). Interestingly, MAPS revealed a significant overlap between peptides that promiscuously bind multiple MHCII alleles and antibody neutralization sites. This overlap was also observed for rotavirus outer capsid glycoprotein VP7, suggesting a deeper relationship between B cell and CD4+ T cell specificity which can facilitate the design of broadly protective vaccines to Zika and other viruses.
Compression and Query Execution within Column Oriented Databases

Compression is a known technique used by many database management systems(“DBMS”) to increase performance[4, 5, 14]. However, not much research has been done in how compression can be used within column oriented architectures. Storing data in column increases the similarity between adjacent records, thus increase the compressibility of the data. In addition, compression schemes not traditionally used in row-oriented DBMSs can be applied to column-oriented systems. This thesis presents a column-oriented query executor designed to operate directly on compressed data. We show that operating directly on compressed data can improve query performance. Additionally, the choice of compression scheme depends on the expected query workload, suggesting that for ad-hoc queries we may wish to store a column redundantly under different coding schemes. Furthermore, the executor is designed to be extensible so that the addition of new compression schemes does not impact operator implementation. The executor is part of a larger database system, known as CStore [10]. Thesis Supervisor: Samuel Madden Title: Assistant Professor, Theses Supervisor
Decoding commensal-host communication through genetic engineering of Staphylococcus epidermidis

Commensal skin bacteria elicit potent, antigen-specific immune responses in the skin without barrier breach or visible inflammation. While microbial modulation of immune homeostasis has profound consequences for epithelial health and inflammatory skin diseases, the mechanisms of microbe-immune crosstalk in the skin are largely unknown. A key barrier to mechanistic work has been genetic intractability of one of the most prevalent skin colonists, Staphylococcus epidermidis (S. epidermidis). Here, we develop a novel method to create a library of mutants with defined cell envelope alterations in primary human S. epidermidis isolates. By colonizing mice with these mutants, we uncover bacterial molecules involved in the induction of defined immune signatures. Notably, we show that under conditions of physiologic colonization, S. epidermidis cell envelope glycolipids are sensed by C-type lectin receptors, likely in non-myeloid cells, in conjunction with Toll-like receptors. This combinatorial signaling determines the quality of T cell responses and results in the potential for greater specificity toward commensal microbiota than previously appreciated. Additionally, the microbial molecules required for the colonization-induced immune response are dispensable for T cells responses in a model of S. epidermidis infection, but differentially modulate innate inflammatory responses. Thus, the same microbe uses distinct sets of molecules to signal to the immune system commensal versus pathogenic behavior, and differential sensing of these microbial signals depends on host context.
Context-dependent environmental adaptation of olfactory receptor abundances

Olfactory receptor usage is highly non-uniform, with some receptor types being orders of magnitude more abundant than others. In mammals, the receptor neurons are replaced regularly, and the receptor distribution changes in response to olfactory experience. The observed changes are mysteriously contextdependent, with increased exposure to odorants leading variously to increased, decreased or unchanged abundance of activated receptors. We propose a theoretical model that explains these observations: the receptor distribution is tuned to efficiently encode information about the olfactory environment. This adaptation occurs before olfactory signals are decorrelated, leading to a new regime of efficient coding in which the optimal receptor distribution is sensitive to the global context of the correlated responses of all receptor types in the population. We demonstrate how this effect reproduces the context-dependence seen in experiments. We also show that the optimal receptor distribution can be achieved by following simple dynamical rules for neural birth and death processes.
Car Authentication and Accident IntimationSystem Using GPS and GSM

Human life is more valuable than anything else, timely help is more important than lending a helping hand. This project is one among those which is designed in a way to save human lives in a timely manner. There are three main modules discussed in the project. When a car meets with an accident, immediately the car’s number and the GPS co-ordinates of the location are messaged to the nearby hospitals, thereby ensuring timely help to the needy. When the car is tried to crank, a text message is sent to the owner thereby intimating the status of the car. Acknowledging the text message allows the driver to proceed further to move else the car is immobilized. While during a long drive, if the car’s engine goes faulty. The error signals from the dash board of the car and the GPS co-ordinates are captured and sent to the near-by service centre, thereby saving time. Here the GSM is used to send the text message and the GPS is used to track the exact coordinates of the car. The serial communication interface UART is used for the communication between the Microcontroller (PIC 16F877A), GSM and GPS module. The RS232 communication standard is used for the following purposes. Electrical signal characteristics such as voltage levels, signalling rate, timing and slew-rate of signals, voltage withstand level, short-circuit behaviour. The microcontroller that meets the requirements for the usage of serial data communication and Analog inputs is preferably the PIC 16F877A series, which provides good interrupt capabilities and reliability
End-to-end self-healing SDH/ATM networks

In considering end-to-end self-healing capabilities, various network evolution scenarios have to be looked at. Network evolution scenarios, such as an embedded SDH/SONET network migration to a hybrid STM/ATM network or deployment of a new all-ATM access, have different architecture characteristics, and thus may lead to different self-healing solutions for providing network survivability. This paper reviews the self-healing schemes for the end-to-end network architecture evolution, introduces some new schemes for ATM networks and segment based self-healing strategies to provide flexibility of deploying various survivable network architecture scenarios, and provides a perspective on guiding current and future self-healing network architecture planning.
Intercomparison of ERS-2 and QuikSCAT winds

Since June 1999, two satellite scatterometers are operational. The European Remote Sensing Satellite (ERS-2) scatterometer and the NASA Seawind scatterometer onboard the QuikSCAT satellite, provide estimation of surface wind vectors with high spatial and temporal resolutions, using different frequencies and resolution configurations. The paper presents the intercomparison between measurements inferred from the two sensors. On average, the two wind vectors compare well. The main discrepancies are found for low wind speed (less than 3 m/s). Over a wind speed range from 3 to 20 m/s, the rms values of the wind speed and direction differences are 2 m/s and 20/spl deg/, respectively, and the correlation is as high as 0.95.
Signaling activated by nucleolar localised Notch4 Intracellular Domain underlies protection from genomic damage

The assembly of signaling hierarchies and their spatiotemporal organization together, contribute to diverse signaling outcomes. This is evident in the Notch pathway, which regulates an array of cellular processes, despite a small number of core components. Here, we describe a Notch4 activated signaling cascade, dependent on the nucleolar localization of the Notch4 Intracellular Domain (NIC4), that protects cells from genotoxic damage. Localization was assessed by immune-staining for endogenous Notch4 and visualization by confocal microscopy, in breast cancer cell lines. Live-cell, imaging-based, biophysical analysis of NIC4-GFP expressing cells, indicated unhindered mobility between the nucleolus and nucleoplasm and a stable nucleolar pool of NIC4-GFP. RNAi-mediated ablations, coupled with analysis of recombinant forms of NIC4 with modifications of its nucleolar localization sequence, confirmed nucleolar localization and identified the nucleolar proteins, Nucleolin and Fibrillarin, as key intermediates in the NIC4-activated signaling cascade. The transcriptional control of ribosome biogenesis (47s and 45s pre-rRNA transcription), emerged as another unexpected consequence of the subcellular distribution of NIC4. Taken together, this study describes intrinsic features of NIC4 that confer spatial flexibility and expand the repertoire of Notch4 signaling.
How we became posthuman : virtual bodies in cybernetics, literature, and informatics, N.K. Hayles : book review

The title is already insightful. We in the information sector are involved with the new media. The importance of understanding the issues we are working with has been emphasized. It is of relevance that we understand the new media as well. This publication offers marvellous thoughts and perspectives in this regard. 'An instant classic, Remediation is required reading for anyone interested in the New Media, especially in relation to other forms of representation. This is one you won't want to miss' writes Katherine Hayles.
The Kaufman oculocerebrofacial syndrome protein Ube3b regulates synapse number by ubiquitinating Ppp3cc

Kaufman oculocerebrofacial syndrome (KOS) is a severe autosomal recessive disorder characterized by intellectual disability, developmental delays, microcephaly and characteristic dysmorphisms. Biallelic mutations of UBE3B, encoding for a ubiquitin ligase E3B are causative for KOS. In this report, we characterize neuronal functions of its murine ortholog Ube3b. We show that Ube3b regulates dendritic branching in a cell-autonomous manner. Moreover, Ube3b knockout (KO) neurons exhibit increased density and aberrant morphology of dendritic spines, altered synaptic physiology and changes in hippocampal circuit activity. Dorsal forebrain-specific Ube3b KO animals show impaired spatial learning and alterations in social interactions. We further demonstrate that Ube3b ubiquitinates the catalytic γ-subunit of calcineurin (Ppp3cc), the overexpression of which phenocopies the loss of Ube3b with regard to dendritic spine density. This work provides insights into the molecular pathologies underlying intellectual disability-like phenotypes in a genetic mouse model for KOS.
Seed Viability of Heracleum mantegazzianum (Apiaceae) Is Quickly Reduced at Temperatures Prevailing in Biogas Plants

Heracleum mantegazzianum is an invasive plant species with enormous effect on ecosystems and human health. Mechanical weed management often results in large amounts of biomass. Fermentation in biogas plants can be used for disposal of this biomass contaminated with seeds and for energetic utilization, if spreading of viable seeds with fermentation residues is prevented. Our aim is to quantify the risk of seed survival in mesophilic biogas plants. Seeds were harvested at three ripening stages in central Germany. They were incubated for 0, 0.5, 1, 2, 4, and 8 days at 35 and 42 °C in water baths. Thereafter, seed viability was assessed by a tetrazolium test. Furthermore, germinative capacity of seeds which had passed an incubation of 48 h at 35 °C were tested. After eight days in water bath none of the 1199 tested seeds were viable anymore. The time until half of the seeds died (ED50) ranged from 9 to 65 h, whereby high temperature accelerated the mortality. Germinative capacity was similar to the seed survival rate. The results suggest that fermentation of H. mantegazzianum biomass poses only a low risk of viable seed spread, if the operating temperature of the biogas plant achieves 42 °C and a high retention time is ensured.
A Study on Information Visualization Depicting Life Model and Employed in Interior Design

In respect of interior design service, how to build a service platform that can document the process of the user's joint participation in the design communication and visualize their life model and design requirement is worth of further study and development. Designers need more messages that influence the interaction between the user and design objects in order to produce a design object that complies with the user's experience and meets their expectations. For the purpose of saving designer's time in searching for design data and of emphasizing the method of converting the data acquired from a user's personal life model, data are visualized into design information that contains specific meaning. After the visualized design information is understood by the interior designer, it is further employed and converted to design knowledge, and eventually applied in the real service design. It is believed in this study a joint design method that involves users and interior designers should be developed to allow users' participation in design process. Users may also participate the activity of creation through a joint design process, thus achieving the goal of service optimization.
The HSV-1 immediate early protein ICP22 is a J-like protein required for Hsc70 reorganization during lytic infection

Molecular chaperones and co-chaperones are the most abundant cellular effectors of protein homeostasis, assisting protein folding and preventing aggregation of misfolded proteins. We have previously shown that HSV-1 infection results in the drastic spatial reorganization of the cellular chaperone Hsc70 into nuclear domains called VICE (Virus Induced Chaperone Enriched) domains and that this recruitment is dependent on the viral immediate early protein ICP22. In this paper, we present several lines of evidence supporting the notion that ICP22 functions as a virally encoded co-chaperone (J-protein/Hsp40) functioning together with its Hsc70 partner to recognize and manage aggregated and misfolded proteins. We show that ICP22 results in (i) nuclear sequestration of non-native proteins, (ii) reduction of cytoplasmic aggresomes in cells expressing aggregation-prone proteins and (iii) thermoprotection against heat-inactivation of firefly luciferase. (iv) Sequence homology analysis indicated that ICP22 contains an N-terminal J-domain and a C-terminal substrate binding domain, similar to type II cellular J-proteins. ICP22 may, thus, be functionally similar to J-protein/Hsp40 co-chaperones that function together with their HSP70 partners to prevent aggregation of non-native proteins. This is not the first example of a virus hijacking a function of a cellular chaperone, as SV40 T Antigen was previously shown to contain a J-domain; however, this the first known example of the acquisition of a complete J-like protein by a virus and suggests that HSV has taken advantage of the adaptable nature of J-proteins to evolve a multi-functional co-chaperone that functions with Hsc70 to promote lytic infection. IMPORTANCE Viruses have evolved a variety of strategies to succeed in a hostile environment. The HSV immediate early protein ICP22 plays several roles in the virus life cycle including down-regulation of cellular gene expression, up-regulation of late viral gene expression, inhibition of apoptosis, prevention of aggregation of non-native proteins and the recruitment of a cellular heat shock protein, Hsc70, to nuclear domains. We present evidence that ICP22 resembles a cellular J-protein/HSP40 family co-chaperone, interacting specifically with Hsc70. This is the first known example of the acquisition of a complete J-like protein by a virus and suggests that HSV has evolved to manipulate the host proteostatic machinery during the establishment of lytic infection.
Fault Diagnosis of Rolling Bearings Based on IMF Envelope Sample Entropy and Support Vector Machine

In this paper, a new fault feature extraction method based on Intrinsic Mode Function (IMF) envelope sample entropy (SampEn) is proposed for rolling bearings fault diagnosis. First, the Empirical Mode Decomposition (EMD) method is utilized to decompose the vibration signals self-adaptively into a number of IMFs which represent different frequency bands from high to low. Second, the IMF envelope signals are used to highlight the fault-induced information in a structurally simpler and physically more meaningful way than the original signals. Thus, the shortcoming of SampEn assigning high values to uncorrelated random signals can be overcome. Finally, the IMF envelope SampEn serve as a fault feature vector to be input into multi-class classifier of Support Vector Machine (SVM) for identification of different bearing conditions. The experimental results indicate that the proposed approach based on IMF envelope SampEn can identify different fault types as well as levels of severity effectively and is superior to that based on IMF SampEn.
Phenotypic selection under two contrasting environments in wild sunflower and its crop–wild hybrid

Hybridization is a common phenomenon in plants and can lead to the introgression of alleles from one population into another, generate new hybrid lineages, or cause species extinction. The environmental conditions and the genetic background of the participating populations may influence these outcomes since they can affect the fitness of hybrids, thereby increasing or decreasing the chances of introgression. Thus, it is important to understand the context‐dependent prospects for introgression of alleles into diverse populations and under multiple ecological environments. Crop–wild hybridization presents an opportunity to explore these dynamics in agroecosystems. To this end, we used diverse wild and hybrid sunflowers from across the northern United States as a basis for evaluating variation in morphological traits and assessing context‐dependent selection. These crop–wild hybrids and their wild counterparts were grown under agricultural conditions in the field with and without wheat competition. Interactions between origin and cross type affected expression of early functional traits, while interactions between competition and cross type acted on reproductive traits. A smattering of early and reproductive traits was affected by interactions between cross type and competition that varied by origin (i.e., 3‐way interactions). Seven functional traits, especially number of branches and tertiary head diameter, underwent net and direct directional selection, while six out of these seven traits appear to also be experiencing nonlinear selection dynamics. In general, wild‐like traits were favored under both sets of conditions, while, under wheat competition, some crop‐like traits related to fast growth and primary head diameter became important. These data reaffirm the hypothesis that stressful conditions establish a scenario more suitable for crop introgression and clarify that nonlinear selection dynamics may play a role in this process.