Miracle-dz/UniFAR-FTUs huggingface dataset:
Camptothecin releases P-TEFb from the inactive 7SK snRNP complex

An immediate effect of DNA Topoisomerase I inhibitors camptothecin (CPT) and its derivates is the inhibition of transcription. These fast-acting drugs are believed to inhibit transcription by blocking topoisomerase–mediated relief of DNA supercoiling that occurs during transcription elongation. The CPT effects are commonly considered to be due to a collision between the drug-trapped enzyme on the DNA template and the elongating RNAPII. Here we present evidences that CPT treatment induces an early affect on the positive elongation factor b (P-TEFb). The P-TEFb activity is tightly and dynamically regulated, and a reservoir of P-TEFb is kept in an inactive state in the multisubunit 7SK snRNP. We found that, shortly after treatment, CPT disrupts the large inactive P-TEFB complex, and such effect is reversible and independent from DNA replication. Thus, CPT modulates P-TEFb equilibrium in a manner similar to Flavopiridol (FP), a pan-Cdk inhibitor proposed as chemotherapeutic agents against cancers. We determined that while FP inhibits Cdk9 leading to hypo-phosphorylation of RNA polymerase II, CPT-mediated release of free P-TEFb correlates with a concomitant hyper-phosphorylation of RNAPII, which in turn alters the levels and distribution of the RNAPII along transcribed genes. The findings that CPT affects P-TEFb activity provide a direct evidence of the mechanism of this drug to inhibit transcription.
The Wiltse Paraspinal Approach to the Lumbar Spine Revisited: An Anatomic Study

The paraspinal posterior approach to the lumbar spine initially was described for spinal fusion, particularly for treatment of lumbosacral spondylolisthesis. Despite the technical details described by Wiltse et al, the exact location of the sacrospinalis muscle that must be split remains unclear. We sought to clarify the anatomic description of the paraspinal posterior approach to the lumbar spine, and to provide topographic landmarks for facilitating this surgical approach. Fifty cadavers were dissected using an anatomic transmuscular paraspinal approach. The level of the natural cleavage plane between the multifidus and the longissimus parts of the sacrospinalis muscle was noted, and measurements were taken between this level and the midline at the level of the spinous process of L4. A natural cleavage plane between the multifidus and the longissimus parts of the sacrospinalis muscle was present in all specimens. There was a fibrous separation between the two muscular parts in 88 of 100 cases. The mean distance between the level of the cleavage plane and the midline was 4.04 cm (range, 2.4-7 cm). Small arteries and veins were present at the level of the cleavage plane in all specimens. These vascular landmarks make it easier to locate the muscular cleavage plane and reach the articular and transverse processes during the paraspinal approach.
Matrix model for Web page community

Discovering intrinsic relationships/structures among concerned Web information objects such as Web pages is important for effectively processing and managing Web information. In this work, a set of Web pages that has its own intrinsic structure is called a Web page community. This paper proposes a matrix model to describe relationships among concerned Web pages. Based on this model, intrinsic relationships among pages could be revealed, and in turn a Web page community could be constructed. The issues that are related to this model and its applications are investigated and studied. Some applications based on this model are presented, which demonstrate the potential of this matrix model in different kinds of Web page community construction and information processing.
An automatic depth map generation for 2D-to-3D conversion

In this paper, we propose an automatic algorithm which generates depth map of 2D image in good quality. The depth map is generated by fusing global depth gradient and local depth refinement. Image classification technique and edge-based depth cue are used to obtain the global depth gradient. In addition, image segmentation method and warm/cool color theory are adopted to generate local depth refinement. The proposed algorithm has advantages of good quality and low complexity. After the depth map is generated, the original 2D image or video can be converted to 3D for showing on stereoscopic display devices.
Upregulation of CREM/ICER suppresses wound endothelial CRE-HIF-1α-VEGF-dependent signaling and impairs angiogenesis in type 2 diabetes

Impaired angiogenesis and endothelial dysfunction in type 2 diabetes constitute dominant risk factors for non-healing wounds and most forms of cardiovascular disease. We propose that diabetes shifts the ‘angiogenic balance’ in favor of an excessive anti-angiogenic phenotype. Herein, we report that diabetes impairs in vivo sponge angiogenic capacity by decreasing VEGF expression and fibrovascular invasion, and reciprocally enhances the formation of angiostatic molecules, such as thrombospondins, NFκB and FasL. Defective in vivo angiogenesis prompted cellular studies in cultured endothelial cells derived from subcutaneous sponge implants (SIECs) of control and Goto-Kakizaki rats. Ensuing data from diabetic SIECs demonstrated a marked upregulation in cAMP-PKA-CREB signaling, possibly stemming from increased expression of adenylyl cyclase isoforms 3 and 8, and decreased expression of PDE3. Mechanistically, we found that oxidative stress and PKA activation in diabetes enhanced CREM/ICER expression. This reduces IRS2 cellular content by inhibiting cAMP response element (CRE) transcriptional activity. Consequently, a decrease in the activity of Akt-mTOR ensued with a concomitant reduction in the total and nuclear protein levels of HIF-1α. Limiting HIF-1α availability for the specific hypoxia response elements in diabetic SIECs elicited a marked reduction in VEGF expression, both at the mRNA and protein levels. These molecular abnormalities were illustrated functionally by a defect in various pro-angiogenic properties, including cell proliferation, migration and tube formation. A genetic-based strategy in diabetic SIECs using siRNAs against CREM/ICER significantly augmented the PKA-dependent VEGF expression. To this end, the current data identify the importance of CREM/ICER as a negative regulator of endothelial function and establish a link between CREM/ICER overexpression and impaired angiogenesis during the course of diabetes. Moreover, it could also point to CREM/ICER as a potential therapeutic target in the treatment of pathological angiogenesis.
Compact and Broadband Stacked Microstrip Patch Antenna for Target Scanning Applications

A broadband and compact stacked microstrip patch antenna has been developed using stacked configuration. The antenna comprises two parasitic patches stacked above the driven patch fed by shifted microstrip feed and a step transformer between feed and patch to achieve broadband coupling. Cross polarization has been improved by inserting a vertical slot in the direction of feed. The antenna occupies very low volume of <inline-formula><tex-math notation="LaTeX"> ${\mathbf{0}}. {\mathbf{36}}{\lambda _{{\mathbf{o}}}}\,\times\,{\mathbf{0}}. {\mathbf{39}}{\lambda _{{\mathbf{o}}}}\,\times\,{\mathbf{0}}. {\mathbf{096}}{\lambda _{\mathbf{o}}}$</tex-math></inline-formula> (radiating elements volume), while overall dimensions with ground plane are <inline-formula><tex-math notation="LaTeX"> ${\mathbf{0}}. {\mathbf{7}}{\lambda _{{\mathbf{o}}}}\,\times\,{\mathbf{0}}. {\mathbf{7}}{\lambda _{{\mathbf{o}}}}\,\times\,{\mathbf{0}}. {\mathbf{096}}{\lambda _{\mathbf{o}}}$</tex-math></inline-formula>. The overall bandwidth achieved is 35% (4.9–7.05 GHz) and a peak gain of 8.2 dBi with average gain of 6 dBi. Antenna radiation patterns are quite unidirectional with <inline-formula><tex-math notation="LaTeX"> ${\mathbf{F}}\text{/}{\mathbf{B}} > {\mathbf{21}}$</tex-math></inline-formula> dB and significantly low cross-polarization levels, suitable for target scanning applications. In the class of printed broadband antennas with unbroken ground plane, the proposed antenna achieves minimum volume with good bandwidth and radiation properties.
Congestion-oriented approach in placement for analog and mixed-signal circuits

Placement design is an essential step in VLSI design and the interaction between different modules makes it a complex process, especially for the integration of analog and mixed-signal circuits. The satisfactory placements of these circuits can be achieved by considering a series of constraints such as symmetry, and general placement constraints-alignment, abutment, preplace, boundary, range and maximum separation. Additionally, the placement result determines the routability of the subsequent routing work. Hence, routability is another important issue that should be considered during the placement phase. In this paper, we propose a new approach which expands the size of certain modules by analyzing the net congestion probability in respect of routability and satisfying the mentioned constraints during the placement process for analog and mixed-signal circuits. Experimental results demonstrate the effectiveness and feasibility of our approach in solving the routability-driven placement problem.
Amyloid β Pathology in Alzheimer’s Disease and Schizophrenia

OBJECTIVE: Severe cognitive impairment is common in elderly patients with schizophrenia. Alzheimer’s disease is the main cause of dementia among the elderly. Biochemical and genetic studies suggest that amyloid β-peptide is central in Alzheimer’s disease. The authors examined the possible involvement of amyloid β-peptide in cognitive impairment in schizophrenia. METHOD: Specific antibodies against two major forms of amyloid β-peptide, Aβx-40 and Aβx-42, were used in sandwich enzyme-linked immunosorbent assays to determine the levels of amyloid β-peptide in postmortem brain samples from Alzheimer’s disease patients (N=10), normal elderly comparison subjects (N=11), and schizophrenia patients with (N=7) or without (N=26) Alzheimer’s disease. RESULTS: The levels of amyloid β-peptide were highest in the Alzheimer’s disease patients, followed by the patients with schizophrenia and comparison subjects. The mean Aβx-42 level in the schizophrenia patients without Alzheimer’s disease was similar to that in the com.
Automatic Stem Mapping Using Single-Scan Terrestrial Laser Scanning

The demand for detailed ground reference data in quantitative forest inventories is growing rapidly, e.g., to improve the calibration of the developed models of airborne-laser-scanning-based inventories. The application of terrestrial laser scanning (TLS) in the forest has shown great potential for improving the accuracy and efficiency of field data collection. This paper presents a fully automatic stem-mapping algorithm using single-scan TLS data for collecting individual tree information from forest plots. In this method, the stem points are identified by the spatial distribution properties of the laser points, the stem model is built up of a series of cylinders, and the location of the stem is estimated by the model. The experiment was performed on nine plots with 10-m radius. The stem-location maps measured in the field by traditional methods were used as the ground truth. The overall stem-mapping accuracy was 73%. The result shows that, in a relatively dense managed forest, the majority of stems can be located by the automatic algorithm. The proposed method is a general solution for stem locating where particular plot knowledge and data format are not required.
Optimal burst duration during a facilitated quadriceps femoris contraction.

OBJECTIVE To determine the most efficient burst duty cycle for eliciting an involuntary quadriceps femoris contraction in healthy subjects. This information will allow clinicians to make an informed decision about the optimal burst duty cycle based upon a specific treatment goal. The logical goal for such a treatment choice is to enhance motor unit recruitment in an effort to maintain postoperative or postinjury strength, when voluntary contractions may be less effective. DESIGN AND SETTING Single-group and 5-measures design. All tests were performed in a university laboratory. SUBJECTS Forty-eight healthy subjects (27 men and 21 women; mean age, 26.4 +/- 8.5 years) performed a maximal voluntary isometric contraction (MVIC) on an isokinetic device and received neuromuscular electrical stimulation (NMES) at 5 different burst duty cycles. MEASUREMENTS Subjects first performed an MVIC for knee extension on an isokinetic dynamometer at 60 degrees of knee flexion. NMES surface electrodes were applied to the quadriceps muscle of each subject's dominant leg. The values for the NMES were 2500-Hz carrier frequency, 50-bursts-per-second treatment frequency, amplitude increased to maximum tolerance, and burst duty cycle set to each of the 5 comparison values. The peak isometric force generated by each of the 5 nonvolitional contractions was recorded, along with the maximal charge per burst tolerated by each subject. Force generated was described as percentage of MVIC. Efficiency was the amount of force per burst charge. RESULTS The mean MVIC achieved by the subjects was 553.8 newtons (N). The average force per burst charge generated at 10% burst duty cycle was 132.9 N; at 30%, 104.2 N; at 50%, 93.1 N; at 70%, 52.9 N; and at 90%, 41.3 N. The average efficiency (force per millicoulombs [mC]) at 10% burst duty cycle was the highest at 6.49 N/mC and at 90% was the lowest at 1.05 N/mC. CONCLUSIONS A burst duty cycle of 10% was the most efficient ratio of burst duration to interburst interval duration for eliciting the strongest muscle contraction. Use of this preferred duty cycle enabled only 8 of 48 subjects (16.6%) to achieve 60% MVIC within 1 trial in 1 session of NMES. Twenty-five subjects (52.0%) were able to achieve at least 10% of the MVIC in the same trial period.
Uptake of Neonicotinoid Insecticides by Water-Foraging Honey Bees (Hymenoptera: Apidae) Through Guttation Fluid of Winter Oilseed Rape

Abstract The water-foraging activity of honey bees (Apis mellifera L.) on guttation fluid of seed-coated crops, such as winter oilseed rape (WOR; Brassica napus L.), has not yet been evaluated. We analyzed the uptake of active substances (a.s.) in guttation fluid by evaluating residues of honey-sac contents. In autumn, insecticide residues of up to 130 µg a.s. per liter were released in WOR guttation fluid; this concentration is noticeably lower than levels reported in guttation fluid of seed-coated maize. Until winter dormancy, the concentrations declined to <30 µg a.s. per liter. In spring, residues were linked to prewintered plants and declined steadily until flowering. The maximum release of residues in guttation fluid of seed-coated WOR occurs on the first leaves in autumn when the colonieś water demand decreases. For the first time, proof for the uptake of guttation fluid from seed-coated WOR by honey bees was provided by measuring residues in individual honey-sac contents. In total, 38 out of 204 samples (19%) showed residues of thiamethoxam at concentrations ranging from 0.3 to 0.95 µg per liter while the corresponding concentrations in guttation fluid of WOR varied between 3.6 to 12.9 µg thiamethoxam per liter. The amounts of thiamethoxam we found in the honey sacs of water-foraging honey bees were therefore below the thresholds in nectar and pollen that are considered to have negative effects on honey bees after chronic exposure.
Levels of coenzyme F420, coenzyme M, hydrogenase, and methylcoenzyme M methylreductase in acetate-grown Methanosarcina

Methanosarcina barkeri strain 227 maintained on an acetate medium for 2 years was found to possess hydrogenase, methylcoenzyme M methylreductase, coenzyme F420, and coenzyme M. The levels of these constituents in acetate-grown cells were similar to those found in cells of the same strain grown on methanol or hydrogen and carbon dioxide.
Storyboarding for visual analytics

Analysts wish to explore different hypotheses, organize their thoughts into visual narratives and present their findings. Some developers have used algorithms to ascertain key events from their data, while others have visualized different states of their exploration and utilized free-form canvases to enable the users to develop their thoughts. What is required is a visual layout strategy that summarizes specific events and allows users to layout the story in a structured way. We propose the use of the concept of ‘storyboarding’ for visual analytics. In film production, storyboarding techniques enable film directors and those working on the film to pre-visualize the shots and evaluate potential problems. We present six principles of storyboarding for visual analytics: composition, viewpoints, transition, annotability, interactivity and separability. We use these principles to develop epSpread, which we apply to VAST Challenge 2011 microblogging data set and to Twitter data from the 2012 Olympic Games. We present technical challenges and design decisions for developing the epSpread storyboarding visual analytics tool that demonstrate the effectiveness of our design and discuss lessons learnt with the storyboarding method.
A Computational Framework for Practical Social Reasoning

This article describes a framework for practical social reasoning designed to be used for analysis, specification, and implementation of the social layer of agent reasoning in multiagent systems. Our framework, called the expectation strategy behavior (ESB) framework, is based on (i) using sets of update rules for social beliefs tied to observations (so‐called expectations), (ii) bounding the amount of reasoning to be performed over these rules by defining a reasoning strategy, and (iii) influencing the agent's decision‐making logic by means of behaviors conditioned on the truth status of current and future social beliefs. We introduce the foundations of ESB conceptually and present a formal framework and an actual implementation of a reasoning engine, which is specifically combined with a general (belief–desire–intention‐based) practical reasoning programming system. We illustrate the generality of ESB through select case studies, which show that it is able to represent and implement different typical styles of social reasoning. The broad coverage of existing social reasoning methods, the modularity that derives from its declarative nature, and its focus on practical implementation make ESB a useful tool for building advanced socially reasoning agents.
An Energy-Efficient Cyclic Diversionary Routing Strategy against Global Eavesdroppers in Wireless Sensor Networks

While many protocols for sensor network security provide confidentiality for message content, contextual information usually remains exposed, which can be critical to the mission of the sensor network. In this paper, we propose an energy-efficient cyclic diversionary routing (CDR) scheme against global eavesdroppers for preserving location privacy and maximizing lifetime of wireless sensor networks (WSNs). To ensure no impact on lifetime of WSNs, we minimize the energy consumption of hotspots and generate abundant diversionary routing paths in areas far from sink. To enhance the location privacy preservation, we theoretically figure out the probability of the cyclic interference routings in different areas of the network and statistically achieve an energy consumption balance in the entire network. Analysis and simulation results show that CDR significantly improves the security in source-location privacy preservation without reducing the network lifetime.
Monoclonal Antibody to Shiga Toxin 2 Which Blocks Receptor Binding and Neutralizes Cytotoxicity

ABSTRACT A monoclonal antibody (MAb) was raised against Shiga toxin 2 (Stx2) of Escherichia coli O157:H7. MAb VTm1.1 belonged to the immunoglobulin G1 subclass and had a κ light chain, and it could neutralize the cytotoxic activity of Stx2 and variants derived from patient strains but not that of variants derived from animals. MAb VTm1.1 was shown to bind to the B subunit of these neutralized Stx2s by Western blotting. Comparison of B-subunit amino acid sequences and reactivities to these Stxs suggested six amino acids (Ser30, Ser53, Glu56, Gln65, Asn68, and Asp69) that were candidates for the MAb VTm1.1 epitope. Consequently, five Stx2 mutants (S30N, S53N, E56H, Q65K, and N68Ter) were prepared by site-directed mutagenesis to determine which residue is essential for the epitope. All of these mutants showed cytotoxicity almost equal to that of the wild-type Stx2. Of the five Stx2 mutants, only E56H could not be neutralized by MAb VTm1.1. Western blot analysis also showed that MAb VTm1.1 could not bind to the E56H B subunit. These results indicated that Glu56 is an important residue recognized by MAb VTm1.1. Immunofluorescence analysis further indicated that MAb VTm1.1 inhibits the binding of Stx2 to its receptors. MAb VTm1.1 could be a useful therapeutic agent for Shiga toxin-producingE. coli infection.
An Examination of Dysfunctional Sport Fans: Method of Classification and Relationships with Problem Behaviors

Past examinations of highly identified sports fans have typically focused on the positive aspects of identification with the team in terms of attitudes, participation, attendance at events, merchandise purchases, and other pro-team related behaviors. The current research, however, investigates the dark side of what may be seen as excessive fan identification—characterized by dysfunctional behaviors such as excessive complaining and confronting others at sporting events. This study presents a measure useful in classifying highly identified fans in terms of their dysfunctional nature and delineates associated problem behaviors (viz., event drinking, blasting officials, aberrant media consumption) and differentiating individual characteristics.
Crystal structure of a PIN (PilT N‐terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 Å resolution

Inna Levin, Robert Schwarzenbacher, Rebecca Page, Polat Abdubek, Eileen Ambing, Tanya Biorac, Linda S. Brinen, Jamison Campbell, Jaume M. Canaves, Hsiu-Ju Chiu, Xiaoping Dai, Ashley M. Deacon, Mike DiDonato, Marc-André Elsliger, Ross Floyd, Adam Godzik, Carina Grittini, Slawomir K. Grzechnik, Eric Hampton, Lukasz Jaroszewski, Cathy Karlak, Heath E. Klock, Eric Koesema, John S. Kovarik, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Daniel McMullan, Timothy M. McPhillips, Mitchell D. Miller, Andrew Morse, Kin Moy, Jie Ouyang, Kevin Quijano, Ron Reyes, Fred Rezezadeh, Alyssa Robb, Eric Sims, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Juli Vincent, Frank von Delft, Xianhong Wang, Bill West, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, and Ian A. Wilson* Joint Center for Structural Genomics, Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park California Genomics Institute of the Novartis Research Foundation, San Diego, California San Diego Supercomputer Center, La Jolla, California University of California, San Diego, La Jolla, California Scripps Research Institute, La Jolla, California
Moving evidence to practice: reflections on a multisite academic–practice partnership

ABSTRACTThis paper describes the challenges encountered by an academic team when working with clinical teams to translated knowledge for the purposes of quality improvement in multiple sites. The sites were four differing health care settings in a Northeastern US state: two acute care hospital sites (one rural, one urban), one visiting nurse service and one psychiatric specialty hospital were purposively chosen for the action research study. In conducting this study at these diverse sites the importance of developing relationships and trust, understanding the context and dealing with real world complexities were evident. We conclude with observations and recommendations on important elements for effective knowledge translation work.