gebhart/patrepeval huggingface dataset:
Antidepressant Effect of Optogenetic Stimulation of the Medial Prefrontal Cortex (2010)

Brain stimulation and imaging studies in humans have highlighted a key role for the prefrontal cortex in clinical depression; however, it remains unknown whether excitation or inhibition of prefrontal cortical neuronal activity is associated with antidepressant responses. Here, we examined cellular indicators of functional activity, including the immediate early genes (IEGs) zif268 (egr1), c-fos, and arc, in the prefrontal cortex of clinically depressed humans obtained postmortem. We also examined these genes in the ventral portion of the medial prefrontal cortex (mPFC) of mice after chronic social defeat stress, a mouse model of depression. In addition, we used viral vectors to overexpress channel rhodopsin 2 (a light-activated cation channel) in mouse mPFC to optogenetically drive "burst" patterns of cortical firing in vivo and examine the behavioral consequences. Prefrontal cortical tissue derived from clinically depressed humans displayed significant reductions in IEG expression, consistent with a deficit in neuronal activity within this brain region. Mice subjected to chronic social defeat stress exhibited similar reductions in levels of IEG expression in mPFC. Interestingly, some of these changes were not observed in defeated mice that escape the deleterious consequences of the stress, i.e., resilient animals. In those mice that expressed a strong depressive-like phenotype, i.e., susceptible animals, optogenetic stimulation of mPFC exerted potent antidepressant-like effects, without affecting general locomotor activity, anxiety-like behaviors, or social memory. These results indicate that the activity of the mPFC is a key determinant of depression-like behavior, as well as antidepressant responses.
Structural and functional analysis of the promoter region involved in full expression of the cryIIIA toxin gene of Bacillus thuringiensis (1994)

The promoter region of the cryIIIA toxin gene of Bacillus thuringiensis is composed of at least three domains: an upstream region extending from nucleotide positions -635 to -553 (with reference to the translational start codon of cryIIIA), an internal region extending from nucleotide positions -553 to -367, and a downstream region extending from nucleotide position -367 to +18. Deletion analysis and transcriptional fusions to the lacZ gene indicate that full expression of cryIIIA requires the association of the upstream and the downstream region. Primer extension experiments reveal a major cryIIIA transcript (designated T-129) starting at nucleotide position -129 and another transcript (designated T-558) starting at nucleotide position -558. Mutation in the -35 region of the promoter responsible for the initiation of T-558 indicates that the upstream promoter is essential for full expression of cryIIIA, although not sufficient. Deletion of the DNA region carrying the previously described cryIIIA promoter does not affect full expression of cryIIIA and does not modify the 5' end of T-129. Taken together, these results indicate that the 5' end of T-129 is not a trnascriptional start site. Therefore, we propose that T-129 results from the processing of the mRNA initiated at the upstream promoter (T-558), generating a stable mRNA with a 5' extremity at nucleotide position -129. From primer extension analysis and transcriptional fusions to lacZ, it appears that the upstream promoter is weakly but significantly expressed during the vegetative phase of growth, is activated at the onset of sporulation and remains active at least until t5. However, unlike the promoters of other cry genes, this promoter is similar to sigma A-dependent promoters rather than sporulation-specific promoters. This promoter may therefore be transcribed by the E sigma A form of RNA polymerase. Activation at the onset of sporulation could result from the disappearance of a repressor, or the appearance of a stationary-phase-specific activator.
Multirate Synchronous Sampling of Sparse Multiband Signals (2009)

Recent advances in electro-optical systems make them ideal for undersampling multiband signals with very high carrier frequencies. In this paper, we propose a new scheme for sampling and reconstructing of a multiband sparse signals that occupy a small part of a given broad frequency range under the constraint of a small number of sampling channels. The locations of the signal bands are not known <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a priori</i> . The scheme, which we call synchronous multirate sampling (SMRS), entails gathering samples synchronously at few different rates whose sum is significantly lower than the Nyquist sampling rate. The signals are reconstructed by finding a solution of an underdetermined system of linear equations by applying a pursuit algorithm and assuming that the solution is composed of a minimum number of bands. The empirical reconstruction success rate is higher than obtained using previously published multicoset scheme when the number of sampling channels is small and the conditions for a perfect reconstruction in the multicoset scheme are not fulfilled. The practical sampling system which is simulated in our work consists of three sampling channels. Our simulation results show that a very high empirical success rate is obtained when the total sampling rate is five times higher than the total signal support of a complex signal with four bands. By comparison, a multicoset sampling scheme obtains a very high empirical success rate with a total sampling rate which is three times higher than the total signal support. However, the multicoset scheme requires 14 channels.
Maternal Smoking in Pregnancy and Offspring Depression: a cross cohort and negative control study (2017)

Previous reports suggest that offspring of mothers who smoke during pregnancy have greater risk of developing depression. However, it is unclear whether this is due to intrauterine effects. Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC) from the UK (N = 2,869), the Nord-Trøndelag health study (HUNT) from Norway (N = 15,493), the Pelotas 1982 Birth Cohort Study from Brazil (N = 2,626), and the Swedish Sibling Health Cohort (N = 258 sibling pairs), we compared associations of maternal smoking during pregnancy and mother's partner's smoking during pregnancy with offspring depression and performed a discordant sibling analysis. In meta-analysis, maternal smoking during pregnancy was associated with higher odds of offspring depression (OR 1.20, 95% CI:1.08,1.34), but mother's partner's smoking during pregnancy was not (OR 1.05, 95% CI:0.94,1.17). However, there was only weak statistical evidence that the odds ratios for maternal and mother's partner's smoking differed from each other (p = 0.08). There was no clear evidence for an association between maternal smoking during pregnancy and offspring depression in the sibling analysis. Findings do not provide strong support for a causal role of maternal smoking during pregnancy in offspring depression, rather observed associations may reflect residual confounding relating to characteristics of parents who smoke.
Mechanical restitution and post extrasystolic potentiation of perfused rat heart: quantitative comparison of normal right and left ventricular responses. (1992)

Interval-force relationship of right and left ventricles of the isolated perfused rat heart was quantified by fitting polynomial, linear and mixed linear-exponential functions to the mechanical restitution (MRC) and post extrasystolic potentiation (PESPC) curves. Ventricular maximum developed pressure (Pmax) and its first derivative (dP/dtmax) were used as indices of contractility. MRCs and PESPCs could be separated into two distinct phases: phase A and phase B of MRCs; phase I and phase II of PESPCs. These phases for the right and left ventricle of the rat heart could be explained on the same model of cellular kinetics of the activator calcium, but showed distinct differences from other species. Right and left ventricle inotropic reserve (CRmax), as quantified from the centre of mass of the phase B of MRCs (from normalized Pmax), was (mean +/- SE): 132.4 +/- 2.05% and 132.1 +/- 1.7% at 1 Hz, which increased significantly (P less than 0.001) to 181.0 +/- 5.8% and 182.3 +/- 5.2% at 3.3 Hz, respectively. Linear regression of normalized right ventricle extrasystolic responses on the left ventricle responses gave a high correlation coefficient (typically r2 = 0.97). Time constants of the fitted mechanical restitution (TMRC) and post extrasystolic potentiation (TPESPC) curves were at 1 Hz, TMRC and TPESPC (from normalized dP/dtmax) were (mean +/- SE): 161.6 +/- 10.8 and 159.0 +/- 13.2 ms for right ventricle, and 196.1 +/- 14.5 and 188.3 +/- 10.7 ms for left ventricle, respectively. The results of this study indicate that interval-force relationship of the rat heart, as exemplified by CRmax and time constants of the fitted curves, could provide a useful index for quantifying and comparing right and left ventricular functions.
New amorphous-silicon image sensor for x-ray diagnostic medical imaging applications (1998)

This paper introduces new high-resolution amorphous Silicon (a-Si) image sensors specifically configured for demonstrating film-quality medical x-ray imaging capabilities. The devices utilizes an x-ray phosphor screen coupled to an array of a-Si photodiodes for detecting visible light, and a-Si thin-film transistors (TFTs) for connecting the photodiodes to external readout electronics. We have developed imagers based on a pixel size of 127 micrometer X 127 micrometer with an approximately page-size imaging area of 244 mm X 195 mm, and array size of 1,536 data lines by 1,920 gate lines, for a total of 2.95 million pixels. More recently, we have developed a much larger imager based on the same pixel pattern, which covers an area of approximately 406 mm X 293 mm, with 2,304 data lines by 3,200 gate lines, for a total of nearly 7.4 million pixels. This is very likely to be the largest image sensor array and highest pixel count detector fabricated on a single substrate. Both imagers connect to a standard PC and are capable of taking an image in a few seconds. Through design rule optimization we have achieved a light sensitive area of 57% and optimized quantum efficiency for x-ray phosphor output in the green part of the spectrum, yielding an average quantum efficiency between 500 and 600 nm of approximately 70%. At the same time, we have managed to reduce extraneous leakage currents on these devices to a few fA per pixel, which allows for very high dynamic range to be achieved. We have characterized leakage currents as a function of photodiode bias, time and temperature to demonstrate high stability over these large sized arrays. At the electronics level, we have adopted a new generation of low noise, charge- sensitive amplifiers coupled to 12-bit A/D converters. Considerable attention was given to reducing electronic noise in order to demonstrate a large dynamic range (over 4,000:1) for medical imaging applications. Through a combination of low data lines capacitance, readout amplifier design, optimized timing, and noise cancellation techniques, we achieve 1,000e to 2,000e of noise for the page size and large size arrays, respectively. This allows for true 12-bit performance and quantum limited images over a wide range of x-ray exposures. Various approaches to reducing line correlated noise have been implemented and will be discussed. Images documenting the improved performance will be presented. Avenues for improvement are under development, including higher resolution 97 micrometer pixel imagers, further improvements in detective quantum efficiency, and characterization of dynamic behavior.
Control of mitotic exit by PP2A regulation of Cdc25C and Cdk1 (2007)

Inactivation of maturation-promoting factor [(MPF) Cdk1/Cyclin B] is a key event in the exit from mitosis. Although degradation of Cyclin B is important for MPF inactivation, recent studies indicate that Cdk1 phosphorylation and inactivation occur before Cyclin B degradation and, therefore, also may be important steps in the exit from mitosis. Cdk1 activity is controlled by the Cdc25C phosphatase, which is turned on at the G 2 /M transition to catalyze Cdk1 activation. PP2A:B56δ is a negative regulator of Cdc25C during interphase. We show here that PP2A:B56δ also regulates Cdc25C at mitosis. Failure of PP2A:B56δ to dephosphorylate Cdc25C at mitosis results in prolonged hyperphosphorylation and activation of Cdc25C, causing persistent dephosphorylation and, hence, activation of Cdk1. This constitutive activation of Cdc25C and Cdk1 leads to a delayed exit from mitosis. Consistent with Cdk1 as a major biological target of B56δ, stable knockdown and germ-line mouse KO of B56δ leads to compensatory transcriptional up-regulation of Wee1 kinase to oppose the Cdc25C activity and permit cell survival. These observations place PP2A:B56δ as a key upstream regulator of Cdk1 activity upon exit from mitosis.
Highly π‐Extended Copolymers with Diketopyrrolopyrrole Moieties for High‐Performance Field‐Effect Transistors (2012)

Two donor-acceptor (D-A) copolymer PDVTs based on diketopyrrolopyrole and (E)-2-(2-(thiophen-2-yl)vinyl)thiophene (TVT) units are synthesized for solution-processed field-effect transistors (FETs). The highly π-extended TVT units strengthen the coplanarity of the polymer backbone. FETs based on PDVTs show high mobilities above 2.0 cm(2) V(-1) s(-1) with a current on/off ratio of 10(5)-10(7) , high shelf storage, and operation stability.
Chemical composition of leaf extracts of Stevia rebaudiana Bertoni grown experimentally in Vojvodina (2008)

The chemical composition of leaf extracts of Stevia rebaudiana Bertoni, grown for the first time on an experimental field near Zrenjanin, was examined by GC-MS. The tested plant material was harvested in September of 2002. To analyze the chemical composition of the lipophilic components of the plant leaves, essential oils and ethyl acetate extract were isolated. Qualitative analysis of the essential oil obtained by hydrodistillation showed that among the identified 88 compounds, the majority were mono- and sesquiterpenes (50 types identified). By analysing the ethyl acetate extract, the presence of fatty acids (present as free and as esters), n-alkanes, n-alkenes, cyclic alkanes, alcohols, aldehydes, ketones, etc. was ascertained. Sesquiterpenes prevailed among the terpenes (50 types identified). Further constituents identified in ethyl acetate extract included sterols. Nerol, ?-cyclocitral, safranal, aromadendrene, ?-amorphene and T-muurolol were identified for the first time in this species, with match values over 90 %. Taking into consideration that these terpenes were identified for the first time in this species, it is obvious that Stevia rebaudiana grown in this area possesses certain specific characteristics that can be ascribed to cultivation on a domestic plantation.
Bacteriophage display: Peptide libraries and drug discovery (1994)

Abstract Filamentous bacteriophage can be utilized to display random peptides, cassette mutagenized proteins, or antibodies. Complex bacteriophage display libraries are easily synthesized and screened for binding to target molecules. Target binding bacteriophage are isolated by affinity selection and then amplified via infection of Escherichia coli . After several rounds of enrichment and amplication, the identity of the peptides, cassettes, or antibodies that bind to the target is readily obtained by DNA sequence analysis. This technology has introduced a new dimension to drug screening in that it offers easy access to a large sequence space. The goal of this review is to summarize technological advances and applications of the bacteriophage display systems. © 1994 Wiley‐Less, Inc.
Gut microbial colonisation in premature neonates predicts neonatal sepsis (2012)

Background Neonatal sepsis due to intestinal bacterial translocation is a major cause of morbidity and mortality. Understanding microbial colonisation of the gut in prematurity may predict risk of sepsis to guide future strategies to manipulate the microbiome. Methods Prospective longitudinal study of premature infants. Stool samples were obtained weekly. DNA was extracted and the V6 hypervariable region of 16S rRNA was amplified followed by high throughput pyrosequencing, comparing subjects with and without sepsis. Results Six neonates were 24–27 weeks gestation at birth and had 18 samples analysed. Two subjects had no sepsis during the study period, two developed late-onset culture-positive sepsis and two had culture-negative systemic inflammation. 324 350 sequences were obtained. The meconium was not sterile and had predominance of Lactobacillus, Staphylococcus and Enterobacteriales. Overall, infants who developed sepsis began life with low microbial diversity, and acquired a predominance of Staphylococcus , while healthy infants had more diversity and predominance of Clostridium, Klebsiella and Veillonella . Conclusions In very low birth weight infants, the authors found that meconium is not sterile and is less diverse from birth in infants who will develop late-onset sepsis. Empiric, prolonged antibiotics profoundly decrease microbial diversity and promote a microbiota that is associated not only with neonatal sepsis, but the predominant pathogen previously identified in the microbiome. Our data suggest that there may be a ‘healthy microbiome’ present in extremely premature neonates that may ameliorate risk of sepsis. More research is needed to determine whether altered antibiotics, probiotics or other novel therapies can re-establish a healthy microbiome in neonates.
Enantioselective Total Synthesis of All of the Known Chiral Cleroindicins (C−F): Clarification Among Optical Rotations and Assignments (2009)

Enantioselective syntheses of all of the named chiral members of the cleroindicin family (C-F) are reported. This effort demonstrates the synthetic utility of a 2,4-dihydroxybenzaldehyde as a starting material for natural product synthesis through the use sequential o-quinone methide chemistry and diastereoselective dearomatization. Natural cleroindicin F was shown to be nearly racemic, and an optically pure synthetic sample of cleroindicin F was found to racemize under slightly basic conditions. All other natural chiral cleroindicins are shown to be partially racemic.
A Randomized Double-Blind Placebo-Controlled Trial of Rifaximin in Patients with Abdominal Bloating and Flatulence (2006)

Rifaximin is a safe and effective treatment for abdominal bloating and flatulence, including in IBS patients. Symptom improvement correlates with reduction in H2-breath excretion. Future trials are needed to examine the efficacy of long-term or cyclic rifaximin in functional colonic disorders.
Poly(methylene amine): A Polymer with the Maximum Possible Number of Amino Groups on a Polymer Backbone (2003)

Taken to the limit: The synthesis of a new amino-functionalized polymer containing one amino group on each carbon of the backbone, is presented. This compound, poly(methylene amine), can be considered as the polymer with the highest content of amino functions known.
METABOLISM AND FUNCTIONS OF TRYPANOTHIONE IN THE KINETOPLASTIDA (1992)

Trypanosomatids differ from all other organisms in their ability to conjugate the sulfur-containing tripeptide, glutathione, and the polyamine, spermidine, to form trypanothione [N1,N8-bis(glutathionyl)spermidine]. Together with the NADPH-dependent flavoprotein, trypanothione reductase, the dithiol form of trypanothione provides an intracellular reducing environment in these parasites, substituting for glutathione and glutathione reductase found in the mammalian host. Trypanothione and its related enzymes are involved in defense against damage by oxidants, certain heavy metals, and possibly xenobiotics. Trypanothione and its metabolic precursor, glutathionylspermidine, are also implicated in the modulation of spermidine levels during growth. Several existing trypanocidal drugs interact with the trypanothione system, suggesting that trypanothione metabolism may be a good target for the development of new drugs. The purification and properties of three key enzymes (glutathionylspermidine synthetase, trypanothione synthetase, and trypanothione reductase) are discussed, and the catalytic mechanism, substrate-specificity, and the three-dimensional structure of trypanothione reductase are compared to that of glutathione reductase.
Hsp70 Prevents Activation of Stress Kinases (1997)

Harmful conditions including heat shock, oxidative stress, UV, and so forth cause programmed cell death, whose triggering requires activation of the Jun N-terminal kinase, JNK. High levels of Hsp72, a heat-inducible member of Hsp70 family, protect cells against a variety of stresses by a mechanism that is unclear at present. Here we report that elevated levels of Hsp72 inhibit a signal transduction pathway leading to programmed cell death by preventing stress-induced activation of JNK. Stress-induced activation of another stress-kinase, p38 (HOG1), is also blocked when the level of Hsp72 is increased. Similarly, addition of a purified recombinant Hsp72 to a crude cell lysate reduced p38 kinase activation, while depletion of the whole family of Hsp70 proteins with a monoclonal antibody enhanced such activation. In addition, we have found that accumulation of abnormal proteins in cells upon incubation with amino acid analogs causes activation of JNK and p38 kinases, which can be prevented by overproduction of Hsp72. Taken together, these data suggest that, in regulation of JNK and p38 kinases, Hsp70 serves as a "sensor" of the build-up of abnormal proteins after heat shock and other stresses. The inhibitory effect of an increased level of Hsp70 on JNK appears to be a major contributor to acquired thermotolerance in mammalian cells.
Temperature Sensing by the dsrA Promoter (2003)

Synthesis of the small regulatory RNA DsrA is under temperature control. The minimal dsrA promoter of 36 bp contains sufficient information to ensure such regulation. In vivo, we have analyzed the critical elements responsible for the temperature control of dsrA by using a collection of chimeric promoters combining various elements of the dsrA promoter and the lacUV5 promoter, which does not respond to temperature. Our results favor an RNA polymerase-DNA interaction model instead of a trans-acting factor for temperature regulation. While all of the elements of the dsrA promoter contribute to temperature-sensitive expression, the sequence of the -10 box and the spacer region are the essential elements for the thermal response of the dsrA promoter. The proper context for these promoter elements, including at least one of the flanking elements, the -35 region or the start site region, is also required. Point mutations demonstrate that the sequence of the -10 box imposes constraints on the length and the sequence of the spacer and/or its AT richness, even at low temperature. These results show a complex interdependence of different regions in the promoter for temperature regulation.
Downlink-uplink duality and effective bandwidths (2003)

There is an interesting duality between the uplink and downlink beamforming problems. We exhibit this duality and use it to show that effective bandwidth results obtained for the uplink translate into effective bandwidth results for the downlink. This duality has been observed in a variety of seemingly different contexts in the literature.
alpha 1-Adrenergic Receptor Subtypes (1994)

Due to the massive data sets available for drug candidates, modern drug discovery has advanced to the big data era. Central to this shift is the development of artificial intelligence approaches to implementing innovative modeling based on the dynamic, ...Read More