Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein-binding dynamics imaged in a living cell

Historically, rate constants were determined in vitro and it was unknown whether they were valid for in vivo biological processes. Here, we bridge this gap by measuring binding dynamics between a pair of proteins in living HeLa cells. Binding of a β-lactamase to its protein inhibitor was initiated by microinjection and monitored by Förster resonance energy transfer. Association rate constants for the wild-type and an electrostatically optimized mutant were only 25% and 50% lower than in vitro values, whereas no change in the rate constant was observed for a slower binding mutant. These changes are much smaller than might be anticipated considering the high macromolecular crowding within the cell. Single-cell analyses of association rate constants and fluorescence recovery after photobleaching reveals a naturally occurring variation in cell density, which is translated to an up to a twofold effect on binding rate constants. The data show that for this model protein interaction the intracellular environment had only a small effect on the association kinetics, justifying the extrapolation of in vitro data to processes in the cell.
Antibiotic Toxicity and Absorption in Zebrafish Using Liquid Chromatography-Tandem Mass Spectrometry

Evaluation of drug toxicity is necessary for drug safety, but in vivo drug absorption is varied; therefore, a rapid, sensitive and reliable method for measuring drugs is needed. Zebrafish are acceptable drug toxicity screening models; we used these animals with a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method in a multiple reaction monitoring mode to quantify drug uptake in zebrafish to better estimate drug toxicity. Analytes were recovered from zebrafish homogenate by collecting supernatant. Measurements were confirmed for drugs in the range of 10–1,000 ng/mL. Four antibiotics with different polarities were tested to explore any correlation of drug polarity, absorption, and toxicity. Zebrafish at 3 days post-fertilization (dpf) absorbed more drug than those at 6 h post-fertilization (hpf), and different developmental periods appeared to be differentially sensitive to the same compound. By observing abnormal embryos and LD50 values, zebrafish embryos at 6 hpf were considered to be suitable for evaluating embryotoxicity. Also, larvae at 3 dpf were adapted to measure acute drug toxicity in adult mammals. Thus, we can exploit zebrafish to study drug toxicity and can reliably quantify drug uptake with LC-MS/MS. This approach will be helpful for future studies of toxicology in zebrafish.
Evaluation of the Deltoid Complex in Supination External Rotation Ankle Fractures

We present the results of a prospective study of supination external rotation ankle injuries with an isolated fibula fracture on plain radiographs. The purpose of this study was to see if a correlation exists between the preoperative evaluation and the intraoperative arthroscopic evaluation of the deltoid ligament complex in these injuries. Gravity stress radiographs of the ankle were evaluated to assess deltoid ligament competence. If the medial clear space was > 4 millimeters, injury to the deltoid ligament complex was assumed. We correlated stress radiograph measurements of the medial clear space with arthroscopic evaluation of the deltoid ligament at the time of open reduction internal fixation in 19 patients. Arthroscopic findings demonstrated that of the 19 patients that underwent open reduction internal fixation, 2 (10%) had intact deltoid ligaments, 2 (10%) had partial ruptures, and 15 (79%) had complete rupture of the deltoid ligament. After placement of fixation, the medial clear space on stress gravity films was measured again to confirm reduction.
Chatting, befriending, and bullying: Adolescent internet experiences and associated psychosocial outcomes.

Over the past 10 years, internet use has become an integral part of adolescent socialization. Teenagers use the internet to communicate with known others as well as with strangers. They engage in online entertainment in the form of gaming and surfing the web. While adolescents mainly use the internet to maintain pre-existing friendships, some adolescents make close friendships online. They also encounter negativity online in the form of cyberbullying. Despite the pervasiveness of internet use, relatively little is known about long-term effects of internet activities on adolescent psycho-social adjustment. This group of studies aimed to identify change over time associated with various aspects of internet use. First, the long-term associations between different internet-based activities and adolescent social relationships were identified. Second, the differences between adolescents who form close internet-based friendships and those who do not were examined. Finally, the importance of internet-based bullying was identified. Overall, results suggest that while some internet-based activities are associated with increased positive effects, some internet activities are also associated with negative outcomes over the long term. Having close online friends as part of one’s peer group is associated with negative psychosocial factors. Cyberbullying was identified as a form of bullying that is associated with many important outcomes. The implications of these findings call for an increase in monitoring, involving not only supervision but direct communication, of adolescents’ internet activities, and increased communication in families about internet use.
Fitting Construal to Judgment: The Compatibility Effect of Regulatory Focus and Level of Construal

This research examines the relationship between regulatory focus and level of construal. Results from six studies show that those with a promotion focus are oriented toward construing information at a higher and more abstract level, whereas those with a prevention focus are oriented toward construing information at a lower, more concrete level (Studies 1 – 3). This fit between regulatory focus and construal level has a positive effect on judgment. Participants perceive greater value (Study 4) and have more favorable attitudes toward a target (Study 5) when it is described at a construal level that fits with their regulatory focus. Participants also exhibit a stronger preference for switching to an alternative when there is a fit between their regulatory focus, the merits of the alternative and the level of construal at which the merits are represented (Study 6).
Localization Algorithm for a Mobile Robot using iGS

As an absolute positioning system, iGS is designed based on ultrasonic signals whose speed can be formulated clearly in terms of time and room temperature, which is utilized for mobile robot localization. The iGS is composed of an RFID receiver and an ultra-sonic transmitter, where an RFID is designated to synchronize the transmitter and receiver of the ultrasonic signal. The traveling time of the ultrasonic signal has been used to calculate the distance between the iGS system and a beacon which is located at a pre-specified location. This paper suggests an effective operation method of iGS to estimate position of the mobile robot working in an unstructured environment. To expand recognition range and to improve accuracy of the system, two strategies are proposed: auto-calibration of beacons belonging to neighboring blocks and removal of the environment-reflected ultrasonic signals. As the results, the ubiquitous localization system based on the iGS as a pseudo-satellite system has been developed successfully with a low cost, a high update rate, and relatively high precision.
Cluster-Buster: finding dense clusters of motifs in DNA sequences

The signals that determine activation and repression of specific genes in response to appropriate stimuli are one of the most important, but least understood, types of information encoded in genomic DNA. The nucleotide sequence patterns, or motifs, preferentially bound by various transcription factors have been collected in databases. However, these motifs appear to be individually too short and degenerate to enable detection of functional enhancer and silencer elements within a large genome. Several groups have proposed that dense clusters of motifs may diagnose regulatory regions more accurately. Cluster-Buster is the third incarnation of our software for finding clusters of pre-specified motifs in DNA sequences. We offer a Cluster-Buster web server at http://zlab.bu. edu/cluster-buster/.
Development of Gallium Compounds for Treatment of Lymphoma: Gallium Maltolate, a Novel Hydroxypyrone Gallium Compound, Induces Apoptosis and Circumvents Lymphoma Cell Resistance to Gallium Nitrate

Clinical studies have shown gallium nitrate to have significant antitumor activity against non-Hodgkin's lymphoma and bladder cancer, thus indicating that gallium-based drugs have potential for further development as antineoplastic agents. In this study, we compared the cytotoxicity of gallium maltolate, a novel gallium compound, with gallium nitrate in lymphoma cell lines, including p53 variant and unique gallium nitrate-resistant cells. We found that gallium maltolate inhibited cell proliferation and induced apoptosis through the mitochondrial pathway at lower concentrations and more rapidly than gallium nitrate. Gallium maltolate produced an increase in intracellular reactive oxygen species (ROS) within 2 h of incubation with cells; this effect could be blocked by mitoquinone, a mitochondria-targeted antioxidant. The role of the transferrin receptor (TfR) in gallium maltolate's action was examined using monoclonal antibody (MoAb) 42/6 to block TfR function. However, although MoAb 42/6 reduced gallium maltolate-induced caspase-3 activity, it had only a minor effect on cell growth inhibition. Importantly, gallium maltolate induced apoptosis in cells resistant to gallium nitrate, and, unlike gallium nitrate, its cytotoxicity was not affected by cellular p53 status. Cellular gallium uptake was greater with gallium maltolate than with gallium nitrate. We conclude that gallium maltolate inhibits cell proliferation and induces apoptosis more efficiently than gallium nitrate. Gallium maltolate is incorporated into lymphoma cells to a greater extent than gallium nitrate via both TfR-independent and -dependent pathways; it has significant activity against gallium nitrate-resistant cells and acts independently of p53. Further studies to evaluate its antineoplastic activity in vivo are warranted.
The Turkish version of the Social Vulnerability Scale: The study of validity and reliability

Article History: Received 16.08. 2013 Received in revised form 24.02. 2014 Accepted 26.11. 2014 Available online Tarih girmek icin burayi tiklatin. The aim of this research is to adapt the Social Vulnerability Scale (Pinsker, Stone, Pachana, & Greenspan, 2006) to Turkish and to examine its psychometric properties. The research was conducted on 661 university students in Sakarya University and Agri Ibrahim Cecen University. Kaiser-Meyer-Olkin (KMO) measure of sampling adequacy of . 95 and a significant result on Bartlett’s test of Sphericity χ2=500,498 (p<.001, df=105). Results confirmatory factor analyses demonstrated that 15 items yielded two factor as original form and that the two-dimensional model was well fit (χ2= 283.21, df= 84, RMSEA= .075, CFI= .99, IFI= .99, NFI= .98, RFI= .97, GFI= .92, SRMR= .043). Factor loadings ranged from . 41 to . 91. Cronbach alpha internal consistency coefficient was found as . 94 for whole scale, . 87 for sub-dimension of gullibility, . 93 for subdimension of credulity. In the concurrent validity significant relationships (r= .34) were found between the Social Vulnerability Scale and Psychological Vulnerability Scale. Test-retest reliability coefficient was . 80 for whole scale. Corrected item-total correlations ranged from . 38 to . 87. Overall results demonstrated that Social Vulnerability Scale can be named as a valid and reliable instrument that could be used in the field of psychology and education. © 2015 IOJES. All rights reserved
A blind speech enhancement algorithm for the suppression of late reverberation and noise

This paper proposes a new speech enhancement algorithm for the suppression of background noise and late reverberation without a priori knowledge. A generalized spectral weighting rule based on estimations for the spectral variances of the late reverberant speech and background noise is used for speech enhancement. This allows to suppress speech distortions due to late room reflections without knowledge about the complete room impulse response. In contrast to existing methods, all needed quantities are estimated entire blindly from the reverberant and noisy speech signal. The new algorithm has also a low signal delay which is important, e.g., for speech enhancement in mobile communication devices or hearing aids.
The neurodynamics of visual search

We review different functions in visual perception associated with attention and memory that have been integrated by a model based on the biased competition hypothesis. The model integrates, in a unifying form, the explanation of several existing types of experimental data obtained at different levels of investigation. At the microscopic level, single cell recordings are simulated. At the mesoscopic level of cortical areas, results of functional magnetic resonance imaging (fMRI) studies are reproduced. Finally, at the macroscopic level, the outcome of psychophysical experiments like visual search tasks are also described by the model. In particular, the model directly addresses how bottom-up and top-down processes interact in visual cognition, and shows how some apparently serial processes reflect the operation of interacting parallel distributed systems. Attentional top-down bias guides the dynamics to focus attention at a given spatial location or on given features.
In Vitro Differentiation of Adult Bone Marrow Progenitors into Antigen-Specific CD4 Helper T Cells Using Engineered Stromal Cells Expressing a Notch Ligand and a MHC Class II protein

A murine stromal cell line (OP9-DL1) expressing a notch ligand, Delta-like-1, has been shown to be able to drive the differentiation of both murine and human hematopoietic progenitors into T cells in vitro. Further studies showed that hematopoietic progenitors transduced by a retroviral vector to express a human CD8 T cell receptor (TCR) followed by an OP9-DL1 monolayer coculture could generate antigen-specific cytotoxic T lymphocytes (CTLs) in vitro. It remains unknown if a similar method could be applied to produce CD4 helper T cells. In this report, we show that murine adult bone marrow cells transduced with an OT2 CD4 TCR and cocultured with OP9 stromal cells expressing Delta-like-1 can differentiate into antigen-specific CD4 T cells in vitro. These cells are capable of inducing the expression of T cell activation markers and producing cytokines upon stimulation. We have also constructed a new stromal cell line (OP9-DL1-IA b ) ectopically expressing a murine major histocompatibility complex (MHC) class II protein, I-A b , in OP9-DL1 cells. This new line could accelerate the development of TCR-transduced bone marrow cells into CD4 T cells, resulting in cells with an improved capacity to respond to T cell stimulation to secrete cytokines. Taken together, we demonstrate a general and potentially useful method to generate autologous antigen-specific CD4 helper T cells in vitro from easily accessible bone marrow cells.
An information-theoretic cryptanalysis of network coding - is protecting the code enough?

We consider the issue of confidentiality in multicast network coding, by assuming that the encoding matrices, based upon variants of random linear network coding, are given only to the source and sinks. Based on this assumption, we provide a characterization of the mutual information between the encoded data and the two elements that can lead to information disclosure: the matrices of random coefficients and, naturally, the original data itself. Our results, some of which hold even with finite block lengths, show that, predicated on optimal source-coding, information-theoretic security is achievable for any field size without loss in terms of decoding probability. It follows that protecting the encoding matrix is generally sufficient to ensure confidentiality of network coded data.
A one-stage decoder for interpretation of natural speech

Current speech understanding systems are typically designed as multistage systems, although this theoretically gives rise to errors due to early decisions. We present a framework that offers the chance of reducing these errors by an integrated system which directly computes a semantic tree representation from the input speech signal through a token passing based one-stage decoder, called ODINS. In order to limit the complexity of ODINS, we represent all a-priori knowledge consistently by a generalized uniform knowledge model based on a hierarchy of probabilistic transition networks, which also can be n-grams. Our framework includes a method to evaluate the system output using an edit distance based tree matching algorithm. First experiments quantify and confirm the theoretical advantage of the one-stage strategy over a corresponding two-stage approach.
Diffusion tensor tractograghy can affect treatment strategy to remove brain occupying mass lesions

Radical resection of a pathological lesion along with the preservation of eloquent cerebral tissue is the principle goal of neurosurgery. Brain lesions are usually diagnosed by conventional magnetic resonance imaging (MRI), but this method is unable to describe the relationship between lesions and neighboring specific white matter (WM) tracts. Diffusion tensor tractograghy (DTT) is a new sophisticated imaging modality to reveal the neural fibers and their relationships with lesions. In the current study we assess that how diffusion tensor tractograghy can affect on treatment planning in patients afflicted by different types of brain lesions. In this prospective observational study, eight patients with brain mass lesion underwent conventional brain MRI pulse sequences and DTT imaging with 1.5 Tesla system using 64 independent diffusion encoding directions between December 2011 to January 2013.Acquired images were assessed by the neuroradiologist and neurosurgeon. Finally, the treatment strategies were compared using data before and after the tractograghy. The treatment strategy in six patients changed from radiotherapy into the craniotomy by using tractograghy data, in one patient changed from radio surgery to craniotomy and in one patient, neurosurgeon preferred to avoid operation. As we can infer from this study, based on the tractograghy results, the treatment technique may be changed, and the treatment plan could be devised with more accuracy and in case of surgery, may lead to less post-operative neurological deficits and better outcome results.
Atomic-AES v 2.0

Very recently, the Atomic AES architecture that provides dual functionality of the AES encryption and decryption module was proposed. It was surprisingly compact and occupied only around 2605 GE of silicon area and took 226 cycles for both the encryption and decryption operations. In this work we further optimize the above architecture to provide the dual encryption/decryption functionality in only 2060 GE and latency of 246/326 cycles for the encryption and decryption operations respectively. We take advantage of clock gating techniques to achieve Shiftrow and Inverse Shiftrow operations in 3 cycles instead of 1. This helps us replace many of the scan flip-flops in the design with ordinary flip-flops. Furthermore we take advantage of the fact that the Inverse Mixcolumn matrix in AES is the cube of the forward Mixcolumn matrix. Thus by executing the forward Mixcolumn operation three times over the state, one can achieve the functionality of Inverse Mixcolumn. This saves some more gate area as one is no longer required to have a combined implementation of the Forward and Inverse Mixcolumn circuit.
An outer approximation based branch and cut algorithm for convex 0-1 MINLP problems

A branch and cut algorithm is developed for solving convex 0-1 Mixed Integer Nonlinear Programming (MINLP) problems. The algorithm integrates Branch and Bound, Outer Approximation and Gomory Cutting Planes. Only the initial Mixed Integer Linear Programming (MILP) master problem is considered. At integer solutions Nonlinear Programming (NLP) problems are solved, using a primal-dual interior point algorithm. The objective and constraints are linearized at the optimum solution of these NLP problems and the linearizations are added to all the unsolved nodes of the enumeration tree. Also, Gomory cutting planes, which are valid throughout the tree, are generated at selected nodes. These cuts help the algorithm to locate integer solutions quickly and consequently improve the linear approximation of the objective and constraints held at the unsolved nodes of the tree. Numerical results show that the addition of Gomory cuts can reduce the number of nodes in the enumeration tree.
Extracting Semantic Relationships between Terms: Supervised vs. Unsupervised Methods

As the amount of electronic documents (corpora, dictionaries, newspapers, newswires, etc.) becomes more andmore important and diversiﬁed, there is a need to extract inf ormation automatically from these texts.In order to extract terms and relations between terms, two methods can be used. The ﬁrst method is theunsupervised approach, which requires a term extraction module and few predeﬁned t ypes, especially termtypes, in order to ﬁnd relationships between terms and to ass ign appropriate types to the relationships.Works on automatic term recognition usually involve predeﬁ nition of a set of term patterns, extractionprocedure and a scoring mechanism to ﬁlter out non-relevant candidates. Smadja (1993) describes a set oftechniques based on statistical methods for retrieving collocations from large text collections. Daille (1996)presents a combination of linguistic ﬁlters and statistica l methods to extract two-word terms. This work imple-ments ﬁnite automata for each term pattern, then various sta tistical scores for ranking the extracted terms arecompared.Unsupervised identiﬁcation of term relationships is a more complicated task, reported in works from variousﬁelds including Computational Linguistics and Knowledge D iscovery in Texts. A keyword-based model for textmining is described in Feldman and Dagan (1995). The work suggests to use a wide range of KDD (KnowledgeDiscovery in Databases) operations on collections of textual documents, including association discovery amongkeywords within the documents. Cooper and Byrd (1997) reports the T
Investigation of Plasma Immersion Ion Implantation Process in Magnetic Mirror Geometry

Plasma immersion ion implantation (PIII) with low external magnetic field has been investigated both numerically and experimentally. The static magnetic field considered is essentially nonuniform and is generated by two magnetic coils installed outside the vacuum chamber. Experiments have been conducted to investigate the effect of two of the most important PIII parameters: target voltage and gas pressure. In that context, it was found that the current density increased when the external parameters were varied. Later, the PIII process was analyzed numerically using the 2.5-D computer code KARAT. The numerical results show that the system of crossed E × B fields enhances the PIII process. The simulation showed an increase of the plasma density around the target under the operating and design conditions considered. Consequently, an increase of the ion current density on the target was observed. All these results are explained through the mechanism of gas ionization by collisions with electrons drifting in crossed E × B fields.