Miracle-dz/UniFAR-FTUs huggingface dataset:
Essential Role of PKCδ in Apoptosis Induction of Mouse Thymocytes

The family of protein kinases C (PKCs) has been implicated in signal transmission leading to apoptosis induction and/or survival. These effects are cell type and tissue dependent. Numerous studies employing phorbol ester, a pleiotropic PKC activator, strongly implicated PKC in apoptosis induction of thymocytes. However, phorbol esters activate both, the conventional PKCs (PKCα, β, γ) as well as the novel PKCs (δ, e, η and θ), the PKC isotype(s) selectively involved in this process have not been established. In this study we used selective pharmacological PKC inhibitors and our established set of PKC knockout mice to define the PKC isotype that is involved in cell death induction of thymocytes. Pharmacological inhibition of nPKCs and in particular gene ablation of PKCδ, results in a profound reduction of p53-dependent as well as independent apoptosis induction. In strict contrast, loss of conventional PKCs as well as loss of two other thymocyte-expressed nPKC family members, PKCe and PKCθ, does not significantly affect thymocyte apoptosis. Taken together, we define an essential and non-redundant pro-apoptotic role of PKCδ in regulating distinct signaling mechanisms that are required to provoke apoptosis of mouse double positive thymocytes in vitro.
Reduced autobiographical memory specificity as an avoidant coping style.

OBJECTIVE Previous studies suggest that reduced autobiographical memory specificity might serve as a way of regulating affect. This study examined the relationship between autobiographical memory specificity and avoidant coping. METHOD Sixty students completed the Autobiographical Memory Test (AMT). Different types of avoidant coping were assessed using questionnaires: the Acceptance and Action Questionnaire, the Cognitive-Behavioural Avoidance Scale and the White Bear Suppression Inventory. RESULTS For all questionnaires, a significant correlation was observed between the number of specific responses on the AMT and an avoidant coping style. More avoidance was associated with fewer specific answers. These correlations remained when corrected for number of omissions. CONCLUSION The results provide further evidence for the affect-regulating quality of autobiographical memory specificity.
Letting the client speak: drug misusers and the process of help seeking.

Summary This is the third report on a study of 150 drug misusers new to treatment at three London drug treatment agencies: a Drug Treatment Clinic, a Therapeutic Community and a Drug Crisis Centre. The focus here is on the clients’perceptions of the help seeking process, and particularly on their reasons for coming to services and their fears about treatment. Analysis of responses revealed an underlying structure to the‘reasons’and‘fears’. There were significant between-agency differences, and differences between those who injected drugs and those who did not. The importance of mood disturbance in the help-seeking process is discussed. The implications of the findings for the development of strategies and the provision of earlier and more appropriate treatment are examined.
Polyphyletic origin of the small-bodied, high-arctic subspecies of tundra reindeer (Rangifer tarandus).

In order to investigate the origin of the three small-bodied, high-arctic subspecies of reindeer, Rangifer tarandus pearyi (the Canadian Archipelago), R. t. eogroenlandicus (East Greenland, extinct since 1900 AD), and R. t. platyrhynchus (Svalbard), samples were collected at nine localities from all six of the currently recognized subspecies of the tundra reindeer. A 203-bp-long fragment of the mitochondrial control region was sequenced from 113 reindeer (Rangifer tarandus). The now extinct subspecies R. t. eogroenlandicus was for the first time included in a molecular study; DNA was extracted from four museum specimens (skins and bones) and successfully sequenced. A polyphyletic origin for the three subspecies of small-bodied, high-arctic reindeer is suggested, with R. t. pearyi and R. t. eogroenlandicus being closely related and probably having evolved in high-arctic North America and R. t. platyrhynchus from Svalbard having evolved from Eurasian large-bodied reindeer. The small-bodied, high-arctic reindeer presumably represent ecotypes that have evolved convergently in similar high-arctic environments.
Detection versus Discrimination of Visual Orientation

The role of focused attention in vision is examined. Recent theories of attention hypothesize that serial search by focal attention is required for discrimination between different combinations of features. Experiments are reported which show that the mixture of a few (less than five) horizontal and vertical line segments embedded in an aggregate of diagonal line segments can be rapidly counted (also called ‘subitizing’) by a parallel (preattentive) process, while the discrimination between horizontal and vertical orientation requires serial search by shifting focal attention to each line segment. Thus detecting and counting targets that differ in orientation can be done in parallel by a preattentive process, whereas knowing ‘what’ the orientation of a target is (horizontal or vertical, ie of a single conspicuous feature) requires a serial search by focal attention.
Allorecognition Histocompatibility in a Protochordate Species: Is the Relationship to MHC Somatic or Structural?

Colonial tunicates are complex marine invertebrates (in fact protochordates) that undergo a variety of histocompatibility reactions in their intraspecific competition for feeding surfaces. By means of these reactions colonies fuse with kin, extend domination over a feeding surface, while isolating unrelated conspecifics. The primary determinant of fusion (with kin) or rejection (of non-kin) is a single, highly polymorphic, histocompatibility gene locus (or haplotype), called Fu/HC. Following fusion with nonidentical kin sharing 1 or more Fu/HC allele(s), the fused pair expands both chimeric partners via an asexual budding process, further extending domination over a feeding surface. However, at some later time point an intense set of histoincompatibility reactions occurs between fused kin, resulting in the destruction of all individuals of one of the genotypes, ending the chimeric state. In this review we describe what is known of the genetics and several biological properties encoded by the Fu/HC, and the several independent gene loci that control the colony resorption phenomena that return the colony to the province of a single genotypic individual.
Modeling of Defects in Integrated Circuit Photolithographic Patterns

In a previous paper by the same author the foundation was laid for the theory of photolithographic defects in integrated circuits. This paper expands on the earlier one and shows how to calculate the critical areas and probability of failure for dense arrays of wiring. The results are used to determine the nature of the defect size distribution with electronic defect monitors. Several statistical techniques for doing this are described and examples are given.
Direct endosomal acidification by the outwardly rectifying CLC‐5 Cl−/H+ exchanger

The voltage‐gated Cl− channel (CLC) family comprises cell surface Cl− channels and intracellular Cl−/H+ exchangers. CLCs in organelle membranes are thought to assist acidification by providing a passive chloride conductance that electrically counterbalances H+ accumulation. Following recent descriptions of Cl−/H+ exchange activity in endosomal CLCs we have re‐evaluated their role. We expressed human CLC‐5 in HEK293 cells, recorded currents under a range of Cl− and H+ gradients by whole‐cell patch clamp, and examined the contribution of CLC‐5 to endosomal acidification using a targeted pH‐sensitive fluorescent protein. We found that CLC‐5 only conducted outward currents, corresponding to Cl− flux into the cytoplasm and H+ from the cytoplasm. Inward currents were never observed, despite the range of intracellular and extracellular Cl− concentrations and pH used. Endosomal acidification in HEK293 cells was prevented by 25 μm bafilomycin‐A1, an inhibitor of vacuolar‐type H+‐ATPase (v‐ATPase), which actively pumps H+ into the endosomal lumen. Overexpression of CLC‐5 in HEK293 cells conferred an additional bafilomycin‐insensitive component to endosomal acidification. This effect was abolished by making mutations in CLC‐5 that remove H+ transport, which result in either no current (E268A) or bidirectional Cl− flux (E211A). Endosomal acidification in a proximal tubule cell line was partially sensitive to inhibition of v‐ATPase by bafilomycin‐A1. Furthermore, in the presence of bafilomycin‐A1, acidification was significantly reduced and nearly fully ablated by partial and near‐complete knockdown of endogenous CLC‐5 by siRNA. These data suggest that CLC‐5 is directly involved in endosomal acidification by exchanging endosomal Cl− for H+.
CCL7 and CXCL10 Orchestrate Oxidative Stress-Induced Neutrophilic Lung Inflammation1

Oxidative stress from ozone (O3) exposure augments airway neutrophil recruitment and chemokine production. We and others have shown that severe and sudden asthma is associated with airway neutrophilia, and that O3 oxidative stress is likely to augment neutrophilic airway inflammation in severe asthma. However, very little is known about chemokines that orchestrate oxidative stress-induced neutrophilic airway inflammation in vivo. To identify these chemokines, three groups of BALB/c mice were exposed to sham air, 0.2 ppm O3, or 0.8 ppm O3 for 6 h. Compared with sham air, 0.8 ppm O3, but not 0.2 ppm O3, induced pronounced neutrophilic airway inflammation that peaked at 18 h postexposure. The 0.8 ppm O3 up-regulated lung mRNA of CXCL1,2,3 (mouse growth-related oncogene-α and macrophage-inflammatory protein-2), CXCL10 (IFN-γ-inducible protein-10), CCL3 (macrophage-inflammatory protein-1α), CCL7 (monocyte chemoattractant protein-3), and CCL11 (eotaxin) at 0 h postexposure, and expression of CXCL10, CCL3, and CCL7 mRNA was sustained 18 h postexposure. O3 increased lung protein levels of CXCL10, CCL7, and CCR3 (CCL7R). The airway epithelium was identified as a source of CCL7. The role of up-regulated chemokines was determined by administering control IgG or IgG Abs against six murine chemokines before O3 exposure. As expected, anti-mouse growth-related oncogene-α inhibited neutrophil recruitment. Surprisingly, Abs to CCL7 and CXCL10 also decreased neutrophil recruitment by 63 and 72%, respectively. These findings indicate that CCL7 and CXCL10, two chemokines not previously reported to orchestrate neutrophilic inflammation, play a critical role in mediating oxidative stress-induced neutrophilic airway inflammation. These observations may have relevance in induction of neutrophilia in severe asthma.
Aligned ZnO nanorod arrays growth on GaN QDs for excellent optoelectronic applications

Uniformly aligned ZnO nanorod (NR) arrays grown on GaN quantum dots (QDs) as preferred nucleation sites are imperative for designing field emission emitters, ultraviolet photodetectors and light-emitting diodes for a wide range of new optoelectronic applications. In a recent study (2015 Nanotechnology 26 415601), Qi et al reported a novel method of fabricating ZnO NRs arrays with uniform shape, the density of which is easily tunable by adjusting the density of GaN QDs. This approach opens a door to obtaining a combination of 0D and 1D structures for optoelectronic applications.
RhoA Signaling Is Required for Respiratory Syncytial Virus-Induced Syncytium Formation and Filamentous Virion Morphology

ABSTRACT Respiratory syncytial virus (RSV) is an important human pathogen that can cause severe and life-threatening respiratory infections in infants, the elderly, and immunocompromised adults. RSV infection of HEp-2 cells induces the activation of RhoA, a small GTPase. We therefore asked whether RhoA signaling is important for RSV replication or syncytium formation. The treatment of HEp-2 cells with Clostridium botulinum C3, an enzyme that ADP-ribosylates and specifically inactivates RhoA, inhibited RSV-induced syncytium formation and cell-to-cell fusion, although similar levels of PFU were released into the medium and viral protein expression levels were equivalent. Treatment with another inhibitor of RhoA signaling, the Rho kinase inhibitor Y-27632, yielded similar results. Scanning electron microscopy of C3-treated infected cells showed reduced numbers of single blunted filaments, in contrast to the large clumps of long filaments in untreated infected cells. These data suggest that RhoA signaling is associated with filamentous virus morphology, cell-to-cell fusion, and syncytium formation but is dispensable for the efficient infection and production of infectious virus in vitro. Next, we developed a semiquantitative method to measure spherical and filamentous virus particles by using sucrose gradient velocity sedimentation. Fluorescence and transmission electron microscopy confirmed the separation of spherical and filamentous forms of infectious virus into two identifiable peaks. The C3 treatment of RSV-infected cells resulted in a shift to relatively more spherical virions than those from untreated cells. These data suggest that viral filamentous protuberances characteristic of RSV infection are associated with RhoA signaling, are important for filamentous virion morphology, and may play a role in initiating cell-to-cell fusion.
Energy-aware routing in Mobile Ad-Hoc Networks

The next generation communication systems will provide high quality multimedia services in a flexible and efficient manner. As an extension of next generation networks, Mobile Ad Hoc Networks (MANETs) have attracted significant attention amongst researchers. Nodes in a MANET have limited battery power. Hence, ad hoc routing protocols ought to be energy conservative to support real-time multimedia services. In this paper, we propose a proactive routing protocol which gives better performance and satisfies the basic power aware parameters like minimum energy consumption per packet, maximum network lifetime, and minimum variance in the node power levels. We use breadth first search to gather the network topology. From this global information, a least cost path is generated using Dijkstra's shortest path algorithm. This least cost path has better battery resources and is refreshed after some fixed intervals of data packet delivery to keep the variance in residual battery power to minimum. Our simulation results show that the proposed protocol provides good service to different types of media while conserving energy.
EWARDS FOR I MITATION L EARNING

Reward function design and exploration time are arguably the biggest obstacles to the deployment of reinforcement learning (RL) agents in the real world. In many real-world tasks, designing a suitable reward function takes considerable manual engineering and often requires additional and potentially visible sensors to be installed just to measure whether the task has been executed successfully. Furthermore, many interesting tasks consist of multiple steps that must be executed in sequence. Even when the final outcome can be measured, it does not necessarily provide useful feedback on these implicit intermediate steps or sub-goals. To address these issues, we propose leveraging the abstraction power of intermediate visual representations learned by deep models to quickly infer perceptual reward functions from small numbers of demonstrations. We present a method that is able to identify the key intermediate steps of a task from only a handful of demonstration sequences, and automatically identify the most discriminative features for identifying these steps. This method makes use of the features in a pre-trained deep model, but does not require any explicit sub-goal supervision. The resulting reward functions, which are dense and smooth, can then be used by an RL agent to learn to perform the task in real-world settings. To evaluate the learned reward functions, we present qualitative results on two real-world tasks and a quantitative evaluation against a human-designed reward function. We also demonstrate that our method can be used to learn a complex real-world door opening skill using a real robot, even when the demonstration used for reward learning is provided by a human using their own hand. To our knowledge, these are the first results showing that complex robotic manipulation skills can be learned directly and without supervised labels from a video of a human performing the task.
PCR-BASED SPECIFIC DETECTION OF RALSTONIA SOLANACEARUM IN SOIL, SEED AND INFECTED PLANT MATERIAL

DNA-based methods have provided powerful tools to identify and detect microorganisms with high sensitivity and specificity. PCR assay amplifies the DNA of bacterial pathogens, targeting the species-specific sequences in their genome. In the present study an efficient DNA isolation protocol and PCR based detection of bacterial wilt pathogen in soil, seed and infected plant materials has been described. The specific primers 759f/760r was successfully used to detect Ralstonia solanacearum from different sources and predicted 281-bp DNA fragment was obtained. In conclusion, the PCR-based detection method using R. solanacearum specific primer offers a rapid and sensitive method for unambiguous detection of this pathogen in soil, seed and infected tomato plant materials.
Estimation of Entropy Reduction and Degrees of Freedom for Signal for Large Variational Analysis Systems

An algorithm due to Bai et al . (1996) allows accurate estimates to be made of the traces of certain functions of large matrices. We show that, by applying the algorithm in the context of variational data assimilation, it is possible to calculate two important measures of the information provided by observations. Specifically, we calculate the entropy reduction and degrees of freedom for signal produced by assimilating many thousands of observations in a version of the ECMWF four-dimensional variational analysis system. We verify the method by comparing it with explicit calculation for a simplified case with few observations. We describe an alternative (more expensive) method for calculating degrees of freedom for signal, based on an algorithm by Wahba (1995). We show that the estimate produced by this method converges to that produced using Bai et al . ’s algorithm as the number of iterations of its minimization algorithm is increased.
Parallel processing of information about location in the amygdala, entorhinal cortex and hippocampus

The conditioned cue preference paradigm was used to study how rats use extra‐maze cues to discriminate between 2 adjacent arms on an 8‐arm radial maze, a situation in which most of the same cues can be seen from both arms but only one arm contains food. Since the food‐restricted rats eat while passively confined on the food‐paired arm no responses are reinforced, so the discrimination is due to Pavlovian stimulus‐reward (or outcome) learning. Consistent with other evidence that rats must move around in an environment to acquire a spatial map, we found that learning the adjacent arms CCP (ACCP) required a minimum amount of active exploration of the maze with no reinforcers present prior to passive pairing of the extra‐maze cues with the food reinforcer, an instance of latent learning. Temporary inactivation of the hippocampus during the pre‐exposure sessions had no effect on ACCP learning, confirming other evidence that the hippocampus is not involved in latent learning. A series of experiments indentified a circuit involving fimbria‐fornix and dorsal entorhinal cortex as the neural basis of latent learning in this situation. In contrast, temporary inactivation of the entorhinal cortex or hippocampus during passive training or during testing blocked ACCP learning and expression, respectively, suggesting that these two structures co‐operate in using spatial information to learn the location of food on the maze during passive pairing and to express this combined information during testing. In parallel with these processes we found that the amygdala processes information leading to an equal tendency to enter both adjacent arms (even though only one was paired with food) suggesting that the stimulus information available to this structure is not sufficiently precise to discriminate between the ambiguous cues visible from the adjacent arms. Expression of the ACCP in normal rats depends on hippocampus‐based learning to avoid the unpaired arm which competes with the amygdala‐based tendency to enter that arm. In contrast, there is cooperation between amygdala‐ and hippocampus‐based tendencies to enter the food‐paired arm. These independent forms of learning contribute to the rat's ability to discriminate among spatial locations using ambiguous extra‐maze cues. © 2013 Wiley Periodicals, Inc.
Scanning copy number and gene expression on the 16p13.3‐13.2 chromosomal region by the systematic multiplex polymerase chain reaction and reverse transcription‐polymerase chain reaction methods

We developed the systematic multiplex reverse transcription‐PCR (SM RT‐PCR) method that is distinguishable from other multiplex RT‐PCR methods by optimized PCR conditions allowing amplification of sequences that fall within a single exon of genes of similar band intensity using genomic DNA template as a calibration standard. Using an SM RT‐PCR system of proto‐oncogenes and tumor suppressor genes, we previously showed that the SM RT‐PCR system, which was developed for cDNA expression analysis, could also be used for a more exquisite analysis of copy number changes in genomic DNA. Here we report that the SM PCR method semiquantitatively detected less than a two‐fold difference in copy number. Furthermore, we also report the results of subchromosomal scanning of copy number and expression using the SM PCR and SM RT‐PCR methods. We identified and characterized the novel homozygous deletion that spans over 12‐plus genes on 16p13.3‐13.2 in the MDA‐MB‐468 breast cancer cell line.
Dynamic diffusion‐tensor measurements in muscle tissue using the single‐line multiple‐echo diffusion‐tensor acquisition technique at 3T

When diffusion biomarkers display transient changes, i.e. in muscle following exercise, traditional diffusion‐tensor imaging (DTI) methods lack the temporal resolution to resolve the dynamics. This article presents an MRI method for dynamic diffusion‐tensor acquisitions on a clinical 3T scanner. This method, the Single‐Line Multiple‐Echo Diffusion‐Tensor Acquisition Technique (SL‐MEDITATE), achieves a high temporal resolution (4 s) by rapid diffusion encoding through the acquisition of multiple echoes with unique diffusion sensitization and limiting the readout to a single line volume. The method is demonstrated in a rotating anisotropic phantom, a flow phantom with adjustable flow speed and in vivo skeletal calf muscle of healthy volunteers following a plantar flexion exercise. The rotating and flow‐varying phantom experiments show that SL‐MEDITATE correctly identifies the rotation of the first diffusion eigenvector and the changes in diffusion‐tensor parameter magnitudes, respectively. Immediately following exercise, the in vivo mean diffusivity (MD) time courses show, before the well‐known increase, an initial decrease that is not typically observed in traditional DTI. In conclusion, SL‐MEDITATE can be used to capture transient changes in tissue anisotropy in a single line. Future progress might allow for dynamic DTI when combined with appropriate k‐space trajectories and compressed sensing reconstruction. Copyright © 2015 John Wiley & Sons, Ltd.