gebhart/patrepeval huggingface dataset:
TCEB1 promotes invasion of prostate cancer cells (2008)

Amplification of the long arm of chromosome 8 is one of the most recurrent findings in prostate cancer and it is associated with poor prognosis. Several minimal regions of amplification suggest multiple target genes which are yet to be identified. We have previously shown that TCEB1, EIF3S3, KIAA0196 and RAD21 are amplified and overexpressed in prostate cancer and they are located in the 8q area. In this study, we examined the functional effects of these genes to prostate cancer cell phenotype. We overexpressed and inhibited the genes by lentivirus mediated overexpression and RNA interference, respectively. shRNA mediated TCEB1 silencing decreased significantly cellular invasion of PC-3 and DU145 cells through Matrigel. TCEB1 silencing reduced the anchorage-independent growth of PC-3 cells. Similar effects were not seen with any other genes. When overexpressed in NIH 3T3 cells, TCEB1 and EIF3S3 increased the growth rate of the cells. Transcriptional profiling of TCEB1 silenced PC-3 cells revealed decrease of genes involved in invasion and metastasis. Finally, we also confirmed here the overexpression of TCEB1 in hormone-refractory prostate tumors. This study indicates that TCEB1 promotes invasion of prostate cancer cells, is involved in development of hormone-refractory prostate cancer and is thereby a strong candidate to be one of the target genes for the 8q gain.
Towards pharmacogenomics knowledge discovery with the semantic web (2009)

Pharmacogenomics aims to understand pharmacological response with respect to genetic variation. Essential to the delivery of better health care is the use of pharmacogenomics knowledge to answer questions about therapeutic, pharmacological or genetic aspects. Several XML markup languages have been developed to capture pharmacogenomic and related information so as to facilitate data sharing. However, recent advances in semantic web technologies have presented exciting new opportunities for pharmacogenomics knowledge discovery by representing the information with machine understandable semantics. Progress in this area is illustrated with reference to the personalized medicine project that aims to facilitate pharmacogenomics knowledge discovery through intuitive knowledge capture and sophisticated question answering using automated reasoning over expressive ontologies.
Functional Outcome and Quality of Life After Stapled Transanal Rectal Resection for Obstructed Defecation Syndrome (2010)

Despite the described postoperative symptoms, most of which can be treated conservatively, the Transtar procedure is an effective treatment for patients with obstructive defecation syndrome and improves quality of life significantly.
RET inhibition: implications in cancer therapy (2013)

Many multitargeted inhibitors which crossreact with RET have been developed and investigated in clinical trials targeting many cancer indications. In particular, VEGFR/PDGFR inhibitors, widely explored as antiangiogenics, have been intensively studied in thyroid carcinoma patients. Notwithstanding the efficacy observed with such agents, their common clinical activity in thyroid carcinoma is of short duration and includes frequent and severe side effects, limiting their therapeutic action. These findings are discussed and the need for improved, more specific RET-targeting drugs is highlighted.
A robust and modular multi-sensor fusion approach applied to MAV navigation (2013)

It has been long known that fusing information from multiple sensors for robot navigation results in increased robustness and accuracy. However, accurate calibration of the sensor ensemble prior to deployment in the field as well as coping with sensor outages, different measurement rates and delays, render multi-sensor fusion a challenge. As a result, most often, systems do not exploit all the sensor information available in exchange for simplicity. For example, on a mission requiring transition of the robot from indoors to outdoors, it is the norm to ignore the Global Positioning System (GPS) signals which become freely available once outdoors and instead, rely only on sensor feeds (e.g., vision and laser) continuously available throughout the mission. Naturally, this comes at the expense of robustness and accuracy in real deployment. This paper presents a generic framework, dubbed MultiSensor-Fusion Extended Kalman Filter (MSF-EKF), able to process delayed, relative and absolute measurements from a theoretically unlimited number of different sensors and sensor types, while allowing self-calibration of the sensor-suite online. The modularity of MSF-EKF allows seamless handling of additional/lost sensor signals during operation while employing a state buffering scheme augmented with Iterated EKF (IEKF) updates to allow for efficient re-linearization of the prediction to get near optimal linearization points for both absolute and relative state updates. We demonstrate our approach in outdoor navigation experiments using a Micro Aerial Vehicle (MAV) equipped with a GPS receiver as well as visual, inertial, and pressure sensors.
InMnAs magnetoresistive spin-diode logic (2012)

Electronic computing relies on systematically controlling the flow of electrons to perform logical functions. Various technologies and logic families are used in modern computing, each with its own tradeoffs. In particular, diode logic allows for the execution of logic with many fewer devices than complementary metal-oxide-semiconductor (CMOS) architectures, which implies the potential to be faster, cheaper, and dissipate less power. It has heretofore been impossible to fully utilize diode logic, however, as standard diodes lack the capability of performing signal inversion. Here we create a binary logic family based on high and low current states in which the InMnAs magnetoresistive semiconductor heterojunction diodes implement the first complete logic family based solely on diodes. The diodes are used as switches by manipulating the magnetoresistance with control currents that generate magnetic fields through the junction. With this device structure, we present basis logic elements and complex circuits consisting of as few as 10% of the devices required in their conventional CMOS counterparts. These circuits are evaluated based on InMnAs experimental data, and design techniques are discussed. As Si scaling reaches its inherent limits, this spin-diode logic family is an intriguing potential replacement for CMOS technology due to its material characteristics and compact circuits.
Glucose Transport in Crabtree-positive and Crabtree-negative Yeasts (1989)

The kinetic parameters of glucose transport in four Crabtree-positive and four Crabtree-negative yeasts were determined. The organisms were grown in aerobic glucose-limited chemostats at a dilution rate of 0.1 h-1. The results show a clear correlation between the presence of high-affinity glucose transport systems and the absence of aerobic fermentation upon addition of excess glucose to steady-state cultures. The presence of these H+-symport systems could be established by determination of intracellular accumulation of 6-deoxy-[3H]glucose and alkalinization of buffered cell suspensions upon addition of glucose. In contrast, the yeasts that did show aerobic alcoholic fermentation during these glucose pulse experiments had low-affinity facilitated-diffusion carriers only. In the yeasts examined the capacity of the glucose transport carriers was higher than the actual glucose consumption rates during the glucose pulse experiments. The relationship between the rate of sugar consumption and the rate of alcoholic fermentation was studied in detail with Saccharomyces cerevisiae. When S. cerevisiae was pulsed with low amounts of glucose or mannose, in order to obtain submaximal sugar consumption rates, fermentation was already occurring at sugar consumption rates just above those which were maintained in the glucose-limited steady-state culture. The results are interpreted in relation with the Crabtree effect. In Crabtree-positive yeasts, an increase in the external glucose concentration may lead to unrestricted glucose uptake by facilitated diffusion and hence, to aerobic fermentation. In contrast, Crabtree-negative yeasts may restrict the entry of glucose by their regulated H+-symport systems and thus prevent the occurrence of overflow metabolism.
The Opioid System and Temperature Regulation (1988)

Opioid drugs and endogenous opioid peptides exert profound effects on body temperature. The particular effect seen is dependent on species, ambient temperature, degree of restraint imposed on the subject, route of drug administration, and a number of other factors. A major determinant is the opioid receptor type with which the agonist forms a complex. Evidence is accumulating that opioid ligands and opioid receptors play a functional role in thermoregulation, even though the opioid system may not be tonically active. Although further studies are needed to fully define the role and the mechanisms involved, as well as the generality of the role in a variety of species, a reasonable working hypothesis is that mu receptors in the rat and the mouse are involved in responses that result in heat gain, while K receptor activation results in opposite responses. To a large extent, the mu receptors in the rat appear to be located primarily in the brain, while the K receptors are outside the brain and perhaps even outside of the central nervous system. At present there is no evidence of involvement of delta receptors in thermoregulation. A fuller understanding of the opioid system and its role in thermoregulation will have broad clinical implications, as well as provide insights into interactions among the several neurotransmitter systems involved in thermoregulatory control of body temperature.
Kainic acid: insights from a neurotoxin into the pathophysiology of Huntington's disease. (1984)

Kainic acid, a conformationally restricted analog of L-glutamic acid, is a potent neuroexcitant. Consistent with the excitotoxin hypothesis of Olney, intrastriatal injection of kainic acid causes degeneration of neurons with perikarya within the striatum but spares axons passing through or terminating in the region. The striatal kainate lesion shares many neurochemical and histopathologic alterations with those observed in the hereditary neurodegenerative disorder of man, Huntington's Disease. Recent studies on the mechanism of neurotoxicity of kainate indicate that its action is complex and indirect; however, ligand binding studies have revealed specific receptors for kainate. Understanding the fundamental mechanisms involved in excitotoxin action may shed light on the pathophysiology of neurodegenerative disorders such as Huntington's Disease.
Human ovarian cancer, cell lines, and primary ascites cells express the human Mullerian inhibiting substance (MIS) type II receptor, bind, and are responsive to MIS. (1999)

Six human ovarian cancer cell lines and samples of ascites cells isolated from 27 patients with stage III or IV ovarian papillary serous cystadenocarcinoma were studied individually to test whether recombinant human Mullerian inhibiting substance (rhMIS) acts via its receptor. To do these experiments, we scaled up production of rhMIS and labeled it successfully with biotin for binding studies, cloned the human MIS type II receptor for mRNA detection, and raised antibodies to an extracellular domain peptide for protein detection. These probes were first tested on the human ovarian cancer cell lines and then applied to primary ovarian ascites cells. rhMIS inhibited colony growth of five of six cell lines that expressed the human MIS type II receptor mRNA by Northern analysis while not inhibiting receptor-negative COS cells. Flow cytometry performed on MIS-sensitive ovarian cancer cell lines demonstrated specific and saturable binding of rhMIS (Kd = 10.2 nM). Ascites cells from 15 of 27 or 56% of patients tested bound biotinylated MIS (MIS-biotin) and, of the 11 that grew in soft agarose, 9 of 11 or 82% showed statistically significant inhibition of colony formation. Of the 15 patients who bound biotinylated MIS, mRNA was available for analysis from 9, and 8 of 9 expressed MIS type II receptor mRNA by reverse transcription-PCR, showing a statistically significant correlation, compared with binding, by chi2 analysis (P = 0.025). Solid ovarian cancers were positive for the MIS type II receptor protein by immunohistochemical staining, which colocalized with staining for antibody to CA-125 (OC-125). Thus, the detection of the MIS type I receptor by flow cytometry may be a useful predictor of therapeutic response to MIS and may be a modality to rapidly choose patients with late-stage ovarian cancer for treatment with MIS.
Slow relaxational processes in the melting of linear biopolymers: A theory and its application to nucleic acids (1984)

Abstract We treat the problem of the mean time of complete separation of complementary chains of a duplex containing N base pairs. A combination of analytical and computer methods is used to obtain the exact solution in the form of a compact expression. This expression is used to analyze the limits of application of the equilibrium theory of helix–coil transition in oligo‐ and polynucleotides. It also allows the melting behavior of a biopolymer to be predicted when its melting is nonequilibrium. In the case of oligonucleotides for which the equilibrium melting takes place at a high value of the stability constant s , the general expression turns into the equation of Craig, Crothers, and Doty, used by them to determine the rate constant k f of the growth of a helical region from temperature‐jump experiments. For the case of fragmented DNA with N ∼ 10 2 , the melting process is shown to be completely nonequilibrium, and as a result, the observed melting temperature should be higher than that for the equilibrium. A simple equation is obtained that makes possible calculation of the real, “kinetic” melting temperature T k . As N increases, the observed melting temperature should approach the equilibrium value, T m . This analysis has explained quantitatively the peculiar chain‐length dependence of the experimentally observed shift in the DNA melting temperature during fragmentation. A thorough analysis is given of the nonequilibrium effects in the melting process of long DNA molecules ( N ≳ 10 3 ). The main conclusion is that even in the presence of profound hysteresis phenomena, the melting profile observed on heating may differ only slightly from the equilibrium profile.
Overview of the Main Outcomes in Breast Cancer Prevention Trials (2003)

Obstetrical & Gynecological Survey 58(7):p 463-465, July 2003. | DOI: 10.1097/01.OGX.0000074099.38382.13
A systematic review protocol for reporting deficiencies within surgical case series (2015)

CRD42015016145.
Grafting as a Tool in Soybean Breeding1 (1977)

Grafting of soybean [ Glycine Max (L.) Merr.] from different maturity groups was studied to determine its feasability for simplifying crossing. When grafted on early flowering genotypes, scions of later flowering genotypes flowered 21 to 50 days after grafts were made. About 95% of the grafts were successful. The grafting technique appears to be an excellent method of inducing earlier flowering on late genotypes to permit their use in a crossing program. It is also a means of producing seed on genotypes that otherwise flower too late for seed production in a particular geographical area.
Model Enzyme Takes Hydrogen Apart (1995)

Splitting hydrogen into its components is a life-or-death reaction for anaerobic bacteria, and biochemists have long struggled to learn how a crucial enzyme—hydrogenase—carries this out. Now a new model enzyme, a simplified version of hydrogenase, is revealing the steps of hydrogen disassembly.
Single ketamine infusion in bipolar depression resistant to antidepressants: are neurotrophins involved? (2012)

The results confirm an antidepressant effect of ketamine infusion as an add-on to mood-stabilizing drugs in bipolar depression resistant to antidepressant treatment. They may also suggest a possible involvement of BDNF in this effect.
Ultrasonic Baths as Substitutes for Shaking Incubator Baths (1991)

An easily assembled incubation bath for enzyme work is described. The bath is made from commercially available units: an ultrasonic bath of the type used for cleaning and a temperature-controlling device. The device is not only much cheaper, quieter, and more compact than a commercially built shaking-type bath, but is also gives superior mixing of heterogeneous enzyme incubation samples, particularly those containing tissue homogenates or subcellular particles.
Neuronal control of the kidney: Contribution to hypertension (1992)

The renal nerves contribute to hypertension in experimental models of the disease, and appear to play a role in human hypertension. Several lines of evidence indicate that both in spontaneously hypertensive rats and in deoxycorticosterone acetate--NaCl rats, the full development of hypertension is dependent on renal efferent nerves and their induction of excess sodium retention. Renal sensory (afferent nerve) feedback to the central nervous system does not contribute to either of these forms of hypertension. In contrast, renovascular hypertension in rats and aortic coarctation hypertension in dogs are mediated, at least in part, by overactivity of renal afferent nerves and a resultant increase in systemic sympathetic nervous system activity. These forms of hypertension are not associated with sodium retention, and selective sensory denervation of renal afferent nerves by dorsal rhizotomy and total renal denervation result in similar reductions in hypertension. Surprisingly, the renal nerves do not contribute to dietary NaCl exacerbated hypertension in the spontaneously hypertensive rat, dietary NaCl-induced hypertension in the Dahl NaCl-sensitive rat, or the chronic hypertensive and nephrotoxic effects of cyclosporine A therapy in the rat, despite the finding that in all three forms of hypertension, overactivity of the sympathetic nervous system is prominent. Clinical studies indicate that the renal afferent and efferent nerves contribute to hypertension of different etiologies. Together these data point to the complex role that the renal nerves likely play in human essential hypertension.
Cloning and analysis of a novel human putative DNA methyltransferase (1998)

DNA methylation is intricately involved in a variety of cellular processes, such as differentiation, cell cycle progression, X-chromosome inactivation and genomic imprinting. However, little is known about how specific DNA methylation patterns are established and maintained. Previously one mammalian DNA methyltransferase has been described, but there has been considerable speculation about the presence of a second activity capable of methylation. Here we report the identification and characterization of a novel human putative DNA methyltransferase. Using a bioinformatics screen we have identified several expressed sequence tags which show high sequence similarity to the Schizosaccharomyces pombe gene pmt1+. The cDNA for PuMet (for putative DNA methyltransferase) was cloned and the predicted amino acid sequence deduced. The gene is ubiquitously expressed, albeit at low levels. Like several other DNA methyltransferases, the bacterially overexpressed protein is not active in methylation assays.
Retardation of radish leaf senescence by polyamines (1982)

The effect of polyamines and related metabolites on several parameters of leaf senescence was followed in detached radish ( Raphanus sativus L. var. radicular cv. “Giant Butter”) leaves floated on test solutions in darkness. Leaf senescence was accompanied by a marked loss of chlorophyll, which started at 24–48 h of incubation. The polyamines, spermine and spermidine, and the diamines, putrescine and cadaverine, were highly effective in arresting chlorophyll loss over a period of at least 96 h. l ‐arginine, and especially l ‐ornithine, were less active. Polyaminens prevented the marked chlorophyll loss in dark‐incubated leaves, but did not compensate for the moderate chlorophyll loss when the leaves were aged in light. Polyamines were also highly effective in retarding earlier events of leaf senescence, prior to chlorophyll loss: both protein degradation and ribonuclease activity were inhibited by spermidine. Chlorophyll and protein loss in dark‐or light‐incubated suspensions of either “intact” or disrupted chloroplasts was not affected by polyamines. – It is concluded that polyamines are highly effective in preventing chlorophyll loss from detached leaves, possibly by controlling early senescence‐linked events which occur in darkness rather than by direct inhibition of chlorophyll degradation.
Estradiol Is a Potent Protective, Restorative, and Trophic Factor after Brain Injury (2009)

Estrogens are a group of pleiotropic steroid hormones that exhibit diverse mechanisms of action in multiple physiologic systems. Over the past 30 years, biomedical science has begun to appreciate that endogenous estrogens and their receptors display important roles beyond the reproductive system. Our growing appreciation of novel, nonreproductive functions for estrogens has fundamentally contributed to our knowledge of their role in human health and disease. Recent findings from the Women's Health Initiative have caused clinicians and scientists to question whether estrogens are protective factors or risk factors. In light of the dichotomy between basic science and clinical studies, this review will attempt to reconcile differences between them. We will focus on studies from our laboratory and others highlighting the beneficial properties of the most abundant endogenous estrogen, 17beta-estradiol, using in vivo and in vitro models of cerebral ischemia and neuronal injury. These studies demonstrate that 17beta-estradiol powerfully protects the brain using multiple molecular mechanisms that promote: (1) decreased cell death, (2) increased neurogenesis, (3) an enhancement of neurotrophic support, and (4) the suppression of proinflammatory pathways.
Cloning and expression of a new member of the melanocyte-stimulating hormone receptor family (1994)

A new member of the G protein-coupled receptor superfamily has been isolated from an ovine genomic library with a probe generated by the application of the PCR technique, using cDNA synthesized on a mRNA template isolated from the ovine pars tuberalis. This genomic clone encodes a novel receptor of 325 amino acids with seven transmembrane domains. These domains share homology with other members of this family, but the best homology is with the recently cloned human MC-1 (50% in the transmembrane domains) and MC-3 (69% in the transmembrane domains) MSH receptors and the human ACTH (42% in the transmembrane domains) receptor. When this receptor was expressed in Cos7 cells, it was able to bind a potent analogue of alpha-MSH, [Nle4,D-Phe7]-alpha-MSH (NDP-MSH), with high affinity. This binding could be displaced by pro-opiomelanocortin-derived and related peptides, with the order of potency NDP-MSH > alpha-MSH = ACTH > beta-MSH and with no effect of gamma-MSH, delta-MSH or beta-endorphin. The expressed receptor was demonstrated to be functionally coupled to the adenylate cyclase second messenger pathway, with alpha-MSH, beta-MSH and ACTH stimulating cyclic AMP production. The amount of the mRNA for this receptor was found to be very low. The tissue distribution of this receptor could only be observed using the reverse transcription-PCR technique and the receptor was found to be present in a number of somatic tissues. These data indicate that this is a new and distinct member of the melanocortin receptor family.