gebhart/patrepeval huggingface dataset:
Neuron–glia crosstalk in health and disease: fractalkine and CX<sub>3</sub>CR1 take centre stage (2013)

An essential aspect of normal brain function is the bidirectional interaction and communication between neurons and neighbouring glial cells. To this end, the brain has evolved ligand-receptor partnerships that facilitate crosstalk between different cell types. The chemokine, fractalkine (FKN), is expressed on neuronal cells, and its receptor, CX(3)CR1, is predominantly expressed on microglia. This review focuses on several important functional roles for FKN/CX(3)CR1 in both health and disease of the central nervous system. It has been posited that FKN is involved in microglial infiltration of the brain during development. Microglia, in turn, are implicated in the developmental synaptic pruning that occurs during brain maturation. The abundance of FKN on mature hippocampal neurons suggests a homeostatic non-inflammatory role in mechanisms of learning and memory. There is substantial evidence describing a role for FKN in hippocampal synaptic plasticity. FKN, on the one hand, appears to prevent excess microglial activation in the absence of injury while promoting activation of microglia and astrocytes during inflammatory episodes. Thus, FKN appears to be neuroprotective in some settings, whereas it contributes to neuronal damage in others. Many progressive neuroinflammatory disorders that are associated with increased microglial activation, such as Alzheimer's disease, show disruption of the FKN/CX(3)CR1 communication system. Thus, targeting CX(3)CR1 receptor hyperactivation with specific antagonists in such neuroinflammatory conditions may eventually lead to novel neurotherapeutics.
Subcellular Relocalization of a <i>Trans</i>-acting Factor Regulates XIAP IRES-dependent Translation (2007)

Translation of the X-linked inhibitor of apoptosis (XIAP) proceeds by internal ribosome entry site (IRES)-mediated initiation, a process that is physiologically important because XIAP expression is essential for cell survival under conditions of compromised cap-dependent translation, such as cellular stress. The regulation of internal initiation requires the interaction of IRES trans-acting factors (ITAFs) with the IRES element. We used RNA-affinity chromatography to identify XIAP ITAFs and isolated the heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1). We find that hnRNP A1 interacts with XIAP IRES RNA both in vitro and in vivo and that hnRNP A1 negatively regulates XIAP IRES activity. Moreover, XIAP IRES-dependent translation is significantly reduced when hnRNP A1 accumulates in the cytoplasm. Osmotic shock, a cellular stress that causes cytoplasmic accumulation of hnRNP A1, also leads to a decrease in XIAP levels that is abrogated by knockdown of hnRNP A1 expression. These results suggest that the subcellular localization of hnRNP A1 is an important determinant of its ability to negatively regulate XIAP IRES activity, suggesting that the subcellular distribution of ITAFs plays a critical role in regulating IRES-dependent translation. Our findings demonstrate that cytoplasmic hnRNP A1 is a negative regulator of XIAP IRES-dependent translation, indicating a novel function for the cytoplasmic form of this protein.
The use of antilipopolysaccharide (anti-LPS) antibodies in the management of septic shock. A preliminary report. (1984)

Twenty-two patients who were in severe sepsis or in septic shock, some with multiple-system failure, were treated with antilipopolysaccharide (anti-endotoxin) antibodies, given in the form of gammaglobulin or as antibody-rich freeze-dried plasma. Twenty patients responded to the treatment either completely or temporarily. The beneficial effect and the physiological aspects of this treatment as opposed to other suggested treatments in the management of septic shock are discussed.
Design of High Throughput Low Complexity Turbo Codes (2022)

Turbo codes are powerful error-correcting codes that are already part of several wireless technologies. Advanced low complexity turbo coding solutions are necessary for next generation systems that will have peak data rates in excess of 100 Mbps. In a high throughput turbo decoder, a significant hardware problem arises due to the interleaver present in the turbo code. This dissertation analyzes contention-free interleavers that avoid this problem by incorporating the hardware constraints into the interleaver description. It is shown that the fraction of interleavers that are contention-free is small. In spite of this seemingly tight constraint, contention-free inter-window shuffle (IWS) interleavers are designed for the eight-state encoder of the 3GPP turbo code, with performance identical to that of the 3GPP interleavers. Since IWS interleavers have a very low complexity implementation, several block sizes are supportable without incurring a storage penalty. A multiple turbo code (MTC) that consists of a parallel concatenation of four two-state component encoders is also investigated. Due to the reduced number of states, the MTC supports larger block sizes than the eight-state 3GPP turbo code with the same decoder hardware. First, using EXIT chart analysis, puncturing patterns for code rates ranging from 1/4 to 3/4 are found. Next, IWS interleavers to facilitate high throughput decoding are designed based on a summary distance approach. Simulation results indicate that the MTC has a better error floor performance than the 3GPP turbo code. A fixed point model for the decoder is obtained using simulation and analytical methods. A technique to resolve a hardware re-use problem in the decoders is proposed, which leads to a further reduction in complexity. Using computational complexity comparisons, it is shown that the MTC can support four times the block length supported by the 3GPP turbo code. A fair comparison framework is adopted to compare the two codes for equal throughput/complexity, and it is shown that the MTC outperforms the 3GPP turbo code. Therefore, the MTC is proposed as an advanced solution for next generation wireless systems.
Ovary and ovulation: A model conforming the decline in follicle numbers to the age of menopause in women (1996)

The store of primordial follicles in the ovary is fixed before birth and dwindles with age until it is unable to provide enough Graafian stages to sustain menstrual cyclicity. According to a simple bi-exponential model of ageing, the rate of follicle disappearance increases at age 37.5 years (or when 25 000 follicles remain) so that the numbers fall to approximately 1000 at 51 years, the median age of menopause in the population. This study attempts to produce a biologically more realistic model of follicle disappearance and harmonizes follicle dynamics with the distribution of menopausal ages from an American survey. The step-change in the rate of follicle attrition was replaced by a model which assumed that this rate changes more gradually with the size of the follicle store. This produced a distribution of predicted menopausal ages (based on an assumed threshold of 1000 follicles) which was closer to observed data. The fit further improved when the model was modified by having a threshold that varied across the population. Using such a stochastic threshold model for menopause, the number of fertile years remaining could be forecast with an acceptable margin of uncertainty if it ever becomes possible to estimate the size of the follicle store in vivo.
Anticipating manic and depressive transitions in patients with bipolar disorder using early warning signals (2021)

Background. In bipolar disorder treatment, accurate episode prediction is paramount but remains difficult. A novel idiographic approach to prediction is to monitor generic early warning signals (EWS), which may manifest in symptom dynamics. EWS could thus form personalized alerts in clinical care. The present study investigated whether EWS can anticipate manic and depressive transitions in individual patients with bipolar disorder. Methods. Twenty bipolar type I/II patients (with ≥2 episodes in the previous year) participated in ecological momentary assessment (EMA), completing five questionnaires a day for four months (Mean=491 observations per person). Transitions were determined by weekly completed questionnaires on depressive (Quick Inventory for Depressive Symptomatology Self-Report) and manic (Altman Self-Rating Mania Scale) symptoms. EWS (rises in autocorrelation at lag-1 and standard deviation) were calculated in moving windows over 17 affective and symptomatic EMA states. Positive and negative predictive values were calculated to determine clinical utility. Results. Eleven patients reported 1-2 transitions. The presence of EWS increased the probability of impending depressive and manic transitions from 32-36% to 46-48% (autocorrelation) and 29-41% (standard deviation). However, the absence of EWS could not be taken as a sign that no transition would occur in the near future. The momentary states that indicated nearby transitions most accurately (predictive values: 65-100%) were full of ideas, worry, and agitation. Large individual differences in the utility of EWS were found.Conclusions. EWS show theoretical promise in anticipating manic and depressive transitions in bipolar disorder, but the level of false positives and negatives, as well as the heterogeneity within and between individuals and preprocessing methods, currently limit clinical utility.
Simple method for isolation of primordial germ cells from chick embryos (1992)

A simple one step centrifugation method was developed for purification of primordial germ cells (PGCs) of chick embryos. PGCs, constituting less than 0.1% of the total blood cells of stage 13-14 embryos that contained a microliter amount of blood, were concentrated at the interface of a 6.3% (w/v) and 14.4% (w/v) Ficoll bilayer by centrifugation at 800 x g for 30 min. the purity of these PGCs was 86%, which was 22 times that obtained previously.
GLP toxicology study of a fully-human T cell redirecting CD3:EGFRvIII binding immunotherapeutic bispecific antibody (2020)

We recently reported the development of a fully-human, CD3-binding bispecific antibody for immunotherapy of malignant glioma. To translate this therapeutic (hEGFRvIII-CD3- bi-scFv) to clinical trials and to help further the translation of other similar CD3-binding therapeutics, some of which are associated with neurologic toxicities, we performed a good laboratory practice (GLP) toxicity study to assess for potential behavioral, chemical, hematologic, and pathologic toxicities including evaluation for experimental autoimmune encephalomyelitis (EAE). To perform this study, male and female C57/BL6 mice heterozygous for the human CD3 transgene (20/sex) were allocated to one of four designated groups. All animals were administered one dose level of hEGFRvIII-CD3 bi-scFv or vehicle control. Test groups were monitored for feed consumption, changes in body weight, and behavioral disturbances including signs of EAE. Urinalysis, hematologic, and clinical chemistry analysis were also performed. Vehicle and test chemical-treated groups were humanely euthanized 48 hours or 14 days following dose administration. Complete gross necropsy of all tissues was performed, and selected tissues plus all observed gross lesions were collected and evaluated for microscopic changes. This included hematoxylin-eosin histopathological evaluation and Fe-ECR staining for myelin sheath enumeration. There were no abnormal clinical observations or signs of EAE noted during the study. There were no statistical changes in food consumption, body weight gain, or final body weight among groups exposed to hEGFRvIII-CD3 bi-scFv compared to the control groups for the 2- and 14-day timepoints. There were statistical differences in some clinical chemistry, hematologic and urinalysis endpoints, primarily in the females at the 14-day timepoint (hematocrit, calcium, phosphorous, and total protein). No pathological findings related to hEGFRvIII-CD3 bi-scFv administration were observed. A number of gross and microscopic observations were noted but all were considered to be incidental background findings. The results of this study allow for further translation of this and other important CD3 modulating bispecific antibodies.
Synthetic Glycans and Glycomimetics: A Promising Alternative to Natural Polysaccharides (2017)

A large quantity of polysaccharide-derived conjugate vaccines have been developed to combat various pathogenic infections. Another prominent polysaccharide, heparin, is listed as an essential drug by the World Health Organization (WHO) to treat thrombus. One of their common problems is that they all derive from natural polysaccharides. Specifically, capsular polysaccharides are mainly obtained from bacterial fermentation and unfractionated heparin is extracted from animal tissues such as porcine mucosa. The quality of natural polysaccharides is inconsistent and traces of contamination would cause a disaster. By contrast, the use of chemical or chemoenzymatic methods could provide structurally homogeneous and quality-controlled glycans. To date, large numbers of polysaccharide fragments and their analogues have been synthesized and evaluated. Some of them even showed comparable activities to their corresponding natural polysaccharides. Here, the latest advances in these synthetic glycan analogues ranging from carbohydrate-based vaccines, heparin-related therapeutics and glycomimetics of polysaccharides are summarized.
Oleate promotes differentiation of chicken primary preadipocytes <i>in vitro</i> (2014)

In addition to providing energy and constituting cell membrane, fatty acids also play an important role in adipocyte differentiation and lipid metabolism. As an important member of monounsaturated fatty acids, oleate, together with other components, is widely used to induce chicken preadipocyte differentiation. However, it is not clear whether oleate alone can induce chicken preadipocyte differentiation. In the present study, four different treatments were designed to test this question: basal medium, IDX [insulin, dexamethasone and IBMX (isobutylmethylxanthine)], oleate and IDX plus oleate. Cytoplasmic lipid droplet accumulation and mRNA expression for adipogenesis-related genes were monitored. After treatment of oleate on chicken preadipocytes, apparent lipid droplet formation and lipid accumulation were observed, accompanied by increasing expression of PPARγ (peroxisome proliferator-activated receptor-γ) and AFABP (adipocyte fatty acid-binding protein), but decreasing level of GATA2 (GATA-binding protein 2). In contrast, for cells cultured in the basal medium with or without IDX supplementation, lipid droplet barely occurred. These results suggest that exogenous oleate alone can act as an inducer of preadipocyte differentiation into adipocytes.
Multi-domain Processors: Challenges, Design Methods, and Recent Developments (2010)

Multi-domain processors characterized by multiple clock/voltage and power domains are widely used to manage power in modern nano-scale processor designs, especially in large scale multi- or many-core systems that require aggressive power management methodologies. One such example is the 48-core prototype processor recently announced by Intel Corp. In order to understand the challenges and opportunities in this problem space, this tutorial presents a comprehensive overview of advanced design techniques in multi-domain clock and power management for high-performance processors, as well as low power systems-on-chip (SoCs). As the number of components on a single chip and their performance continue to increase, the design of the communication architecture plays a major role. From this perspective, this tutorial addresses the network-on-chip (NoC) design and presents several research issues where the concept of “network” is at the forefront of multi/many-core processing. NoCs are suitable for large high-performance chip multiprocessors as well as SoCs, all of which increasingly employing a multi- domain design style. Consequently, the tutorial surveys asynchronous routers for various architectures and asynchronous interconnections that enable higher bandwidth and lower power. The tutorial will discuss these issues and outline existing approaches to overcome any inherent deficiencies and fully enable the aforementioned technology. In addition to the on-chip communication problem, the twin concern of increased power consumption of future multi/many-core systems needs to be addressed, especially in the presence of workload and parameter variations. For multi-core designs, the concept of multiple voltage/frequency islands (VFIs) is typically used to enable fine-grain power management. In such a system, each island can work at its own speed, while the communication across different VFIs is achieved through mixed clock/mixed voltage FIFOs. We plan to discuss the design and management of novel NoC architectures partitioned into multiple VFIs, as well as online feedback control mechanisms that can dynamically adjust the operating voltage and frequency around some statically prescribed values. Finally, considering variability effects at micro-architecture and architecture levels is needed for determining variation-aware dynamic power management algorithms that are most likely to meet performance and power constraints. Towards this end, we plan to discuss modeling the effects of process variation at micro-architecture/architecture level in modern multi/many-core, multi-domain systems and show how dynamic power management mechanisms can be developed such that these systems behave in a robust manner in the presence of process technology parameter variation. Of extreme importance is the ability to provide workload- and process variability-driven adaptability not only through a static assignment of local voltages/frequencies, but also using dynamic application mapping and on-the-fly voltage/frequency scaling.
Take the Opportunity (2014)

As you read this, we will be approaching our annual conference. I am so excited! We have been changing our annual conference over the last 3 to 4 years in order to provide our members with a better product/experience. Everyone who looked at our conference was surprised at how successful it was, but we wanted to make it even better for the members. And I think we have succeeded-but we need to keep making it better every year.
<i>Salmonella enterica</i> Serovar Typhi Possesses a Unique Repertoire of Fimbrial Gene Sequences (2001)

Salmonella enterica serotype Typhi differs from nontyphoidal Salmonella serotypes by its strict host adaptation to humans and higher primates. Since fimbriae have been implicated in host adaptation, we investigated whether the serotype Typhi genome contains fimbrial operons which are unique to this pathogen or restricted to typhoidal Salmonella serotypes. This study established for the first time the total number of fimbrial operons present in an individual Salmonella serotype. The serotype Typhi CT18 genome, which has been sequenced by the Typhi Sequencing Group at the Sanger Centre, contained a type IV fimbrial operon, an orthologue of the agf operon, and 12 putative fimbrial operons of the chaperone-usher assembly class. In addition to sef, fim, saf, and tcf, which had been described previously in serotype Typhi, we identified eight new putative chaperone-usher-dependent fimbrial operons, which were termed bcf, sta, stb, ste, std, stc, stg, and sth. Hybridization analysis performed with 16 strains of Salmonella reference collection C and 22 strains of Salmonella reference collection B showed that all eight putative fimbrial operons of serotype Typhi were also present in a number of nontyphoidal Salmonella serotypes. Thus, a simple correlation between host range and the presence of a single fimbrial operon seems at present unlikely. However, the serotype Typhi genome differed from that of all other Salmonella serotypes investigated in that it contained a unique combination of putative fimbrial operons.
Polypyrrole:  Diffusion Coefficients and Degradation by Overoxidation (2004)

The electroactivity of electrogenerated polypyrrole films was degraded by applying consecutive anodic potential pulses (overoxidation). After each degradation step, the electroactivity of the material was recorded by voltammetric and chronoamperometric measurements. The charge consumed during each degradation step was calculated by the difference between the degradation and the control chronoamperograms. The diffusion coefficients of the counterions within the material were obtained from the control chronoamperograms by applying the electrochemically stimulated conformational-relaxation model. As the materials became increasingly degraded, slower oxidation processes were observed, and decreasing diffusion coefficients were obtained. These observations point to growing cross linking between neighboring polymeric chains during the degradation process, thus reducing conjugation lengths and increasing the rigidity of the conformational electro-chemo-stimulated movements on the chains. An electroactivity degradation of 50% induces a 15% increase in the weight of the material, pointing to the presence of rigid and oxidized islands entrapped by cross-linking points that prevent any ionic interchanges.
<title>Characterization of laser-induced pressure transients by means of piezoelectric PVDF films</title> (1996)

For an interpretation of pressure signals detected by piezoelectric PVDF-foils several parameters are of importance. These are for example pressure pulse duration and rise times, active area of the film and specifications concerning the high-frequency technique of the experimental setup. Using an input-resistance of 1 M(Omega) at the storage-oscilloscope leads to reflections of the signal which superimpose each other when reflected a second time at the foil. This might cause an apparent increase of the amplitude. The utilization of a longer cable allows a separation of each reflected pulse, but it causes the problem, that the cable's input- impedance approaches its characteristic impedance of 50 (Omega) . This will lead to a time derived signal as well as using 50 (Omega) as input-resistance at the scope. Therefore a direct measurement of short pressure transients requires a very short cable and an input-resistance of 1 M(Omega) . Otherwise the measured signal allows no proportional relation between pressure transient and measured voltage signal. In the latter case a frequency-dependent correction of the signal becomes necessary. This has been developed in this paper by means of Fast Fourier Transform algorithm. After correction in the frequency-domain the signal is transformed back into the time-domain.
Energy-Efficient Transmission for Beamforming in Wireless Sensor Networks (2010)

Energy conservation is essential in wireless sensor networks (WSNs) because of limited energy in batteries. Collaborative beamforming uses multiple transmitters to form antenna arrays; the electromagnetic waves from these antenna arrays can create constructive interferences at the receiver and increase the transmission distance. Each transmitter can use lower power and save energy, since the energy consumption is spread over multiple transmitters. However, if the same nodes are always used for collaborative beamforming, these nodes would deplete their energy much sooner and this sensing area will no longer be monitored. To avoid this situation, energy consumption for collaborative beamforming needs to be balanced over the whole network by assigning the transmitters in turns. The transmitters in each round are selected by a scheduler and the energy carried in each node is balanced to increase the number of transmissions. We define the lifetime of a network as the number of transmissions until a certain percentage of the nodes depletes their energy. This paper proposes an algorithm to calculate energy-efficient schedules based on the remaining energy and the phase differences of their signals arriving at the receiver. Compared with an existing algorithm, our algorithm can extend the network lifetime by more than 60%.