Miracle-dz/UniFAR-FTUs huggingface dataset:
Disparate response of articular- and auricular-derived chondrocytes to oxygen tension

ABSTRACT Purpose/Aim: To determine the effect of reduced (5%) oxygen tension on chondrogenesis of auricular-derived chondrocytes. Currently, many cell and tissue culture experiments are performed at 20% oxygen with 5% carbon dioxide. Few cells in the body are subjected to this supra-physiological oxygen tension. Chondrocytes and their mesenchymal progenitors are widely reported to have greater chondrogenic expression when cultured at low, more physiological, oxygen tension (1–7%). Although generally accepted, there is still some controversy, and different culture methods, species, and outcome metrics cloud the field. These results are, however, articular chondrocyte biased and have not been reported for auricular-derived chondrocytes. Materials and Methods: Auricular and articular chondrocytes were isolated from skeletally mature New Zealand White rabbits, expanded in culture and differentiated in high density cultures with serum-free chondrogenic media. Cartilage tissue derived from aggregate cultures or from the tissue engineered sheets were assessed for biomechanical, glycosaminoglycan, collagen, collagen cross-links, and lysyl oxidase activity and expression. Results: Our studies show increased proliferation rates for both auricular and articular chondrocytes at low (5%) O2 versus standard (20%) O2. In our scaffold-free chondrogenic cultures, low O2 was found to increase articular chondrocyte accumulation of glycosaminoglycan, but not cross-linked type II collagen, or total collagen. Conversely, auricular chondrocytes accumulated less glycosaminoglycan, cross-linked type II collagen and total collagen under low oxygen tension. Conclusions: This study highlights the dramatic difference in response to low O2 of chondrocytes isolated from different anatomical sites. Low O2 is beneficial for articular-derived chondrogenesis but detrimental for auricular-derived chondrogenesis.
The Revolution of Evolution for Real-World Applications.

This paper describes an evolutionary search method known as the genetic algorithm (GA) and examines its application to real-world problems. A description of the algorithm itself and its history is provided. A general review of GA theory and analysis is given, and many of the newer, more advanced types of GA are introduced. Some of the hundreds of different applications tackled by GAs are then described. Two more detailed case-studies are included, to outline how GAs can be applied to real-world applications, and to illustrate some of the difficulties such problems present to the designers of GA-based systems. The paper concludes that the GA is a highly significant and useful tool, suitable for a variety of different applications.
Reducing off-chip memory traffic by selective cache management scheme in GPGPUs

The performance of General Purpose Graphics Processing Units (GPGPUs) is frequently limited by the off-chip memory bandwidth. To mitigate this bandwidth wall problem, recent GPUs are equipped with on-chip L1 and L2 caches. However, there has been little work for better utilizing on-chip shared caches in GPGPUs. In this paper, we propose two cache management schemes: write-buffering and read-bypassing. The write buffering technique tries to utilize the shared cache for inter-block communication, and thereby reduces the DRAM accesses as much as the capacity of the cache. The read-bypassing scheme prevents the shared cache from being polluted by streamed data that are consumed only within a thread-block. The proposed schemes can be selectively applied to global memory instructions using newly defined cache operators. We evaluate the effects of the proposed schemes for a few GPGPU applications by simulations. We have shown that the off-chip memory accesses can be successfully reduced by the proposed techniques. We also analyze the effectiveness of these methods when the throughput gap between cores and off-chip memory becomes wider.
Striatal Fast-Spiking Interneurons: From Firing Patterns to Postsynaptic Impact

In the striatal microcircuit, fast-spiking (FS) interneurons have an important role in mediating inhibition onto neighboring medium spiny (MS) projection neurons. In this study, we combined computational modeling with in vitro and in vivo electrophysiological measurements to investigate FS cells in terms of their discharge properties and their synaptic efficacies onto MS neurons. In vivo firing of striatal FS interneurons is characterized by a high firing variability. It is not known, however, if this variability results from the input that FS cells receive, or if it is promoted by the stuttering spike behavior of these neurons. Both our model and measurements in vitro show that FS neurons that exhibit random stuttering discharge in response to steady depolarization do not show the typical stuttering behavior when they receive fluctuating input. Importantly, our model predicts that electrically coupled FS cells show substantial spike synchronization only when they are in the stuttering regime. Therefore, together with the lack of synchronized firing of striatal FS interneurons that has been reported in vivo, these results suggest that neighboring FS neurons are not in the stuttering regime simultaneously and that in vivo FS firing variability is more likely determined by the input fluctuations. Furthermore, the variability in FS firing is translated to variability in the postsynaptic amplitudes in MS neurons due to the strong synaptic depression of the FS-to-MS synapse. Our results support the idea that these synapses operate over a wide range from strongly depressed to almost fully recovered. The strong inhibitory effects that FS cells can impose on their postsynaptic targets, and the fact that the FS-to-MS synapse model showed substantial depression over extended periods of time might indicate the importance of cooperative effects of multiple presynaptic FS interneurons and the precise orchestration of their activity.
Potentially Inappropriate Medication Use in Individuals with Mild Cognitive Impairment: Results from the Kerala Einstein Study

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Myoendothelial Gap Junctions May Provide the Pathway for EDHF in Mouse Mesenteric Artery

Endothelium-dependent hyperpolarization of vascular smooth muscle provides a major pathway for relaxation in resistance arteries. This can occur due to direct electrical coupling via myoendothelial gap junctions (MEGJs) and/or the release of factors (EDHF). Here we provide evidence for the existence of functional MEGJs in the same, defined branches of BALB/C mouse mesenteric arteries which show robust EDHF-mediated smooth muscle relaxation. Cyclopiazonic acid (CPA, 10 µM) was used to stimulate EDHF in arteries mounted under isometric conditions and constricted with phenylephrine. Simultaneous measurement of smooth muscle membrane potential and tension demonstrated that CPA caused a hyperpolarization of around 10 mV, reversing the depolarization to phenylephrine by 94% and the associated constriction by 66%. The relaxation to CPA was endothelium dependent, associated with the opening of Ca2+-activated K channels, and only in part due to the release of nitric oxide (NO). In the presence of the NO synthase inhibitor, L-NAME (100 µM), the relaxation to CPA could be almost completely inhibited with the putative gap junction uncoupler, carbenoxolone (100 µM). Inhibition of the synthesis of prostaglandins or metabolites of arachidonic acid had no effect under the same conditions, and small rises in exogenous K+ failed to evoke consistent or marked smooth muscle relaxation, arguing against a role for these molecules and ions as EDHF. Serial section electron microscopy revealed a high incidence of MEGJs, which was correlated with heterocellular dye coupling. Taken together, these functional and morphological data from a defined mouse resistance artery suggest that the EDHF response in this vessel may be explained by extensive heterocellular coupling through MEGJs, enabling spread of hyperpolarizing current.
Cooperative Communication to Improve Reliability and Efﬁcient Neighborhood Wakeup in Wireless Sensor Networks

—To maximize lifetime of Wireless Sensor Networks, medium access control protocols usually trade off reliability for energy efﬁciency. Channel errors, collisions, idle listening, and overhearing further aggravate the problem. Our work investigates opportunities to improve reliability in Wireless Sensor Networks under such constraints. We consider a multi-hop data gathering network in which sensor nodes are deployed around a sink. Nodes periodically sense data and forward it to next hop nodes. For such a network, a Medium Access Control protocol, called CPS-MAC, is proposed. This protocol uses cooperative communication to improve reliability by using overhearing to its advantage. In conventional protocols, overhearing causes nodes to receive packets which are not meant for them. Therefore, these packets are discarded and considered a waste of energy. On the contrary, CPS-MAC intentionally wakes up next 1-hop and 2-hop neighbors to improve their chances of overhearing a packet. The overheard packets are buffered and then relayed to the next hop neighbor, combating channel fading by a cooperative spatial diversity gain. By combining multiple copies of the same packet, next hop neighbor is more likely to recover the original packet. Design challenges such as efﬁciently waking up neighborhood nodes, minimizing energy overhead, and partner selection are addressed. Simulation results show that CPS-MAC signiﬁcantly decreases packet error rate without expending additional energy.
Inhibition of Translation by a Short Element in the 5′ Leader of the Herpes Simplex Virus 1 DNA Polymerase Transcript

ABSTRACT Many viruses regulate gene expression, both globally and specifically, to achieve maximal rates of replication. During herpes simplex virus 1 infection, translation of the DNA polymerase (Pol) catalytic subunit is inefficient relative to other proteins of the same temporal class (D. R. Yager, A. I. Marcy, and D. M. Coen., J. Virol. 64:2217-2225, 1990). To investigate the mechanisms involved in the inefficient translation of Pol and to determine whether this inefficient translation could affect viral replication, we performed a mutagenic analysis of the 5′ end of the pol transcript. We found that a short sequence (∼55 bases) in the 5′ leader of the transcript is both necessary and sufficient to inhibit translation in rabbit reticulocyte lysates and sufficient to inhibit reporter gene translation in transfected cells. RNase structure mapping experiments indicated that the inhibitory element adopts a structure that contains regions of a double-stranded nature, which may interfere with ribosomal loading and/or scanning. Pol accumulated to ∼2- to 3-fold-higher levels per mRNA in cells infected with a mutant virus containing a deletion of the ∼55-base inhibitory element than in cells infected with a control virus containing this element. Additionally, the mutant virus replicated less efficiently than the control virus. These results suggest that the inhibitory element regulates Pol translation during infection and that its inhibition of Pol translation is beneficial for viral replication.
Ad 2.0: a novel recombineering platform for high-throughput generation of tailored adenoviruses

Recombinant adenoviruses containing a double-stranded DNA genome of 26–45 kb were broadly explored in basic virology, for vaccination purposes, for treatment of tumors based on oncolytic virotherapy, or simply as a tool for efficient gene transfer. However, the majority of recombinant adenoviral vectors (AdVs) is based on a small fraction of adenovirus types and their genetic modification. Recombineering techniques provide powerful tools for arbitrary engineering of recombinant DNA. Here, we adopted a seamless recombineering technology for high-throughput and arbitrary genetic engineering of recombinant adenoviral DNA molecules. Our cloning platform which also includes a novel recombination pipeline is based on bacterial artificial chromosomes (BACs). It enables generation of novel recombinant adenoviruses from different sources and switching between commonly used early generation AdVs and the last generation high-capacity AdVs lacking all viral coding sequences making them attractive candidates for clinical use. In combination with a novel recombination pipeline allowing cloning of AdVs containing large and complex transgenes and the possibility to generate arbitrary chimeric capsid-modified adenoviruses, these techniques allow generation of tailored AdVs with distinct features. Our technologies will pave the way toward broader applications of AdVs in molecular medicine including gene therapy and vaccination studies.
HOG and Spatial Convolution on SIMD Architecture

In recent years, Histogram of Oriented Gradients (HOG) has gained tremendous popularity in the Computer Vision community. It is a widely used feature in Object Recognition tasks, and is often followed by a classification step. Popular classifiers like SVMs perform a convolution operation in the classification step. Spatial convolution is a building-block in Computer Vision, being used from filters to classifiers. In this report, we present a SIMD implementation on the most generic processors (CPUs), using the most generic instruction set (x86 or x86-64), in a generic language (C++) and target these two very widely used algorithms HOG and convolution. These steps form a performance bottleneck for real-time classification pipelines. As a way to test our system, we implement the entire testing pipeline of the Exemplar-SVM [17]. We hope that our implementations serve a large audience in speedy research.
Convex Invariance Learning

Invariance and representation learning are important precursors to modeling and classi-ﬁcation tools particularly for non-Euclidean spaces such as images, strings and non-vectorial data. This article proposes a method for learning invariances in data while jointly estimating a model. The technique re-sults in a convex programming problem with a consistent and unique solution. Representation variables are considered as aﬃne transformations conﬁned by multiple equality and inequality constraints. These interact individually with each datum yet maintain the overall solvability of the model estimation process while uniquely solving for the representational variables themselves. The method is applicable to various types of modeling, including maximum likelihood estimation, principal components analysis, and discriminative methods. Starting from aﬃne invariance, several types of invariances are proposed and implemented as convex programs including clustering, permutation, selection, rotation, and translation. Experiments on non-vectorial data such as images and collections of tuples provide promising results.
Relative Efficiency of Biological Transmission of Anaplasma marginale (Rickettsiales: Anaplasmataceae) by Dermacentor andersoni (Acari: Ixodidae) Compared with Mechanical Transmission by Stomoxys calcitrans (Diptera: Muscidae)

Abstract Anaplasma marginale Theiler is a tick-borne intraerythrocytic rickettsial pathogen of cattle that also can be mechanically transmitted by biting flies. Rickettsemia during the acute phase of infection may reach as high as 109 infected erythrocytes (IEs) per milliliter of blood. Animals that survive acute infection develop a life-long persistent infection that cycles between 102.5 and 107 IE/ml of blood. We compared stable fly Stomoxys calcitrans (L.)-borne mechanical transmission during acute infection with Rocky Mountain wood tick, Dermacentor andersoni Stiles-borne biological transmission in the persistent phase of infection to demonstrate quantitatively that biological transmission by ticks is considerably more efficient than mechanical transmission by biting flies. Stable flies that partially fed on an acutely infected calf and were immediately transferred to susceptible calves to complete their bloodmeals failed to transmit A. marginale. Ticks that fed on the original acquisition host after it reached the persistent phase of infection (>300-fold lower rickettsemia) successfully transmitted A. marginale after transfer to the same calves that failed to acquire infection after fly feeding. Failure of fly-borne mechanical transmission at a rickettsemia >300-fold higher than that from which ticks transmit with 100% efficiency demonstrates that tick-borne biological transmission is at least 2 orders of magnitude more efficient than direct stable fly-borne mechanical transmission.
Prospective study of body mass index, height, physical activity and incidence of bladder cancer in US men and women

We evaluated prospectively the association between body mass index (BMI), height, recreational physical activity and the risk of bladder cancer among US adults. Data were used from 2 ongoing cohorts, the Health Professionals Follow‐up Study and the Nurses' Health Study, with 3,542,012 years of follow‐up and 866 incident bladder cancer cases (men = 507; women = 359) for the anthropometric analysis and 1,890,476 years of follow‐up and 706 incident bladder cancer cases (men = 502; women = 204) for the physical activity analysis. Cox proportional hazard models were used to estimate incidence rate ratios (RR) and 95% confidence intervals (CI) between BMI, height, physical activity and bladder cancer risk adjusting for age, pack‐years of cigarette smoking and current smoking. Estimates from each cohort were pooled using a random‐effects model. We observed no association between baseline BMI and bladder cancer risk, even when we compared a BMI of ≥30 kg/m2 to a BMI of 18–22.9 kg/m2 [pooled multivariate (MV) RR, 1.16; 95% CI: 0.89–1.52]. A weak, but statistically significant, association was observed for the same comparison after excluding bladder cancer cases diagnosed within the first 4 years of follow‐up (pooled MV RR, 1.33; 95% CI: 1.01–1.76). Height was not related to bladder cancer risk (pooled MV RR, 0.82; 95% CI: 0.65–1.03, top vs. bottom quintile). Total recreational physical activity also was not associated with the risk of bladder cancer (pooled MV RR, 0.97; 95% CI: 0.77–1.24, top vs. bottom quintile). Our findings do not support a role for BMI, height or physical activity in bladder carcinogenesis. © 2006 Wiley‐Liss, Inc.
Instructional Practices in Los Angeles Universal Preschool

As part of Phase 3 of the Universal Preschool Child Outcomes Study (UPCOS-3), Mathematica Policy Research worked with the First 5 LA Children and Families Commission and Los Angeles Universal Preschool (LAUP) to conduct a descriptive study of the characteristics of classrooms in LAUP programs during winter 2010.
Systematic errors of noise parameter determination caused by imperfect source impedance measurement

We present a rigorous two-step analysis of systematic errors in the four-noise parameter determination of a two-port network using the cold-source technique. This analysis is based on an original model that accounts for residual errors in the source impedance measurement. The method employs two linear fractional transforms to decompose the errors into relevant factor sets affecting the parameters in different ways. Analyses performed for a low-noise pseudomorphic high-electron mobility transistor (PHEMT) and a microwave amplifier show that the noise parameters of the low-noise PHEMT are highly vulnerable to such errors.
OmniAD

This paper introduces "OmniAD," a novel data-driven pipeline to model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally, aerodynamics are examined through elaborate wind tunnel experiments or expensive fluid dynamics computations, and are only measured for a small number of discrete wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag and lift, for any incoming wind direction using a novel representation based on spherical harmonics. Our data-driven technique acquires the aerodynamic properties of an object simply by capturing its falling motion using a single camera. Once model parameters are estimated, OmniAD enables realistic real-time simulation of rigid bodies, such as the tumbling and gliding of leaves, without simulating the surrounding air. In addition, we propose an intuitive user interface based on OmniAD to interactively design three-dimensional kites that actually fly. Various non-traditional kites were designed to demonstrate the physical validity of our model.
Visual Support in Intervention for Preschoolers With Specific Language Impairment

This study was conducted as a follow-up analysis to two prior studies using existing data gathered in those original studies. In the current study, we focus on those preschoolers who received one of two interventions that varied in terms of the level of visual supports for grammatical elements (n = 22 of the original 34 participants). Utilizing random selection for intervention, our study examined potential session-to-session differences in rate of progress between two interventions. One intervention provided visual support using color-coded screens and syntactic slots for grammatical and semantic sentence elements (Group 1, Computer-Assisted Intervention, n = 11). The other intervention provided visual support through objects in play, books, and picture cards with actions for semantic elements only (Group 2, Table-Top Intervention, n = 11). Both interventions targeted accurate production of a basic simple sentence (i.e., third person singular present progressive sentences). Twenty-two, 3- to 5-year-old preschoolers with specific language impairment (SLI) participated in 20-minute once weekly sessions. Both interventions included sentence breakdown (i.e., breaking sentences into subject, verb, object components that are trained to an 80% criterion) and build-up (i.e., putting the entire sentence together). Rate of progress in intervention was monitored for (a) efficiency (first session that the 80% criterion was achieved) and (b) syntactic growth (movement beyond the basic simple sentence level). Blinded assessors scored session-to-session data to establish potential differences in rate of progress between groups. The results showed that Group 1 outperformed Group 2 for efficiency and syntactic growth. This study demonstrated that use of multiple visual supports in expressive grammar training facilitated a therapeutic advantage in session-to-session grammatical learning for preschoolers with SLI.