gebhart/patrepeval huggingface dataset:
Regulation of Gene Expression in Diverse Cyanobacterial Species by Using Theophylline-Responsive Riboswitches (2014)

Cyanobacteria are photosynthetic bacteria that are currently being developed as biological production platforms. They derive energy from light and carbon from atmospheric carbon dioxide, and some species can fix atmospheric nitrogen. One advantage of developing cyanobacteria for renewable production of biofuels and other biological products is that they are amenable to genetic manipulation, facilitating bioengineering and synthetic biology. To expand the currently available genetic toolkit, we have demonstrated the utility of synthetic theophylline-responsive riboswitches for effective regulation of gene expression in four diverse species of cyanobacteria, including two recent isolates. We evaluated a set of six riboswitches driving the expression of a yellow fluorescent protein reporter in Synechococcus elongatus PCC 7942, Leptolyngbya sp. strain BL0902, Anabaena sp. strain PCC 7120, and Synechocystis sp. strain WHSyn. We demonstrated that riboswitches can offer regulation of gene expression superior to that of the commonly used isopropyl-β-d-thiogalactopyranoside induction of a lacI(q)-Ptrc promoter system. We also showed that expression of the toxic protein SacB can be effectively regulated, demonstrating utility for riboswitch regulation of proteins that are detrimental to biomass accumulation. Taken together, the results of this work demonstrate the utility and ease of use of riboswitches in the context of genetic engineering and synthetic biology in diverse cyanobacteria, which will facilitate the development of algal biotechnology.
Stent migration to the ileum—A potentially lethal complication after montgomery salivary bypass tube placement for hypopharyngeal stenosis after laryngectomy (2010)

To avoid potentially lethal complications associated with MSBT migration into the intestinal tract, we recommend secure fixation of the MSBT to a nasogastric tube.
Bounds on the time to reach agreement in the presence of timing uncertainty (1991)

Abstract : Upper and lower bounds are proved for the time complexity of the problem of reaching agreement in a distributed network, in the presence of process failures and inexact information about time. It is assumed that the amount of (real) time between any two consecutive steps of any nonfaulty process is at least sub1 and at most sub2; thus, C = sub1/sub2 is a measure of the timing uncertainty. It is also assumed that the time for message delivery is at most d. Processes are assumed to fail by stopping, so that process failures can be detected by timeouts. A straightforward adaption of an (function + 1)-round round-based agreement algorithm takes time (function + 1)Cd if there are function faults, while a straightforward reduction from a timing-based algorithm to a round-based algorithm yields a lower bound of (function + 1)d. The first major results major result of this paper is an agreement algorithm in which the uncertainty factor C is only incurred for one round, yielding a running time of approximately 2 function d + Cd in the worst case. The second major result shows that any agreement algorithm must take time at least (function - 1)d + Cd in the worst case. The new agreement algorithm can also be applied in a model where processors are synchronous (C = 1), and where message delay during a particular execution of the algorithm is bounded above by a quantity delta which could be smaller than the worst-case upper bound d. The running time in this case is approximately (2 function - 1)delta + d.
Weight loss in hypertrophic cardiomyopathy: A clinical case series (2023)

Obesity is prevalent among patients with hypertrophic cardiomyopathy (HCM). Obese HCM patients have greater wall thickness, LV mass, worse hemodynamic function and NYHA class. Weight loss may favorably influence the HCM phenotype. We describe six patients with hypertrophic cardiomyopathy who lost weight through diet and lifestyle changes (n = 4) or bariatric surgery (n = 2). Radiographic imaging, with cardiac MRI or CT scan, was performed before and after their weight loss. There was a mean decrease in LV mass and indexed LV mass, and a mean numerical decrease in mean wall thickness in up to 14 out of 18 LV segments. There was also NYHA class reduction in symptoms. In this case series, we have shown that substantial weight loss in HCM patients can be associated with a decrease in LV mass, wall thickness and improvement in symptoms. These observations indicate the potential for positive remodeling of the heart by weight loss. Prospective studies of the benefits of weight loss in HCM are needed.
Evaluating the progress of Deep Reinforcement Learning in the real world: aligning domain-agnostic and domain-specific research (2021)

Deep Reinforcement Learning (DRL) is considered a potential framework to improve many real-world autonomous systems; it has attracted the attention of multiple and diverse fields. Nevertheless, the successful deployment in the real world is a test most of DRL models still need to pass. In this work we focus on this issue by reviewing and evaluating the research efforts from both domain-agnostic and domain-specific communities. On one hand, we offer a comprehensive summary of DRL challenges and summarize the different proposals to mitigate them; this helps identifying five gaps of domain-agnostic research. On the other hand, from the domain-specific perspective, we discuss different success stories and argue why other models might fail to be deployed. Finally, we take up on ways to move forward accounting for both perspectives.
THE EFFECTS OF INDUCED MUSCULAR TENSION AND ORIGINAL MUSCULAR TENSION IN VERBAL LEARNING (1970)

The purpose of this experiment was to study the effects of experimentally induced muscular tension (IMT), original spontaneous muscular tension (MT) which each subject had usually in laboratory, upon verbal learning. The main problem points were as follows.(1) Does IMT affect learning or recall?(2) Does High-MT facilitate recall more than Low-MT?(3) Is there an interaction between the effects of IMT and MT?(4) Does IMT-during-learning (T-T, T-N groups) affect recall even on the following trials?Experiment I: Subjects (Ss) were 48 undergraduate students. A Hull-type memory drum, presenting each word for a 3 sec. duration, was used. A list consisted of 12 nonsense syllables. A weight hand dynamometer, evoking IMT, was used. Ss pulled the dynamometer at a value of 1/5 maximum tension determined for each S. The Ss' task was to learn 12 nonsense syllables. Time intervals between list presentation and recall were 0, 100, 200 and 360 sec. Ss were required to recall words freely as many as possible. Group T-T learned and recalled under IMT. Group T-N learned under IMT and recalled under no IMT. Group N-T learned under no IMT and recalled under IMT. Group N-N learned and recalled under no IMT. As a measure of MT, eye blink rates were measured during 5 learning trials. With this measure, each of four IMT group was further divided into two subgroups: high muscular tension group (H-MT) and low muscular tension group (L-MT). After 4 free recall trials, Ss were required to relearn to a learning criterion.Experiment II: Ss were 40 undergraduate students and were divided into four IMT groups (T-T, T-N, N-T, N-N). Ss were shown only once a list consisting of 7 paired Japanese verbs. The temporal intervals between stimuli presentation and recall were 0, 60, 120 and 180sec. Eyeblink rates were not measured. Otherwise the procedure was nearly equal to that of Exp. I.The main results were as follows.(1) In both Exp. I and Exp. II, recall was facilitated in the groups under IMT (T-T, N-T), as compared with the results of the groups under no IMT (T-N, N-N) (Figs. 2 & 6). Thus IMT failed to have an effect upon habit formation.(2) Recall in group H-MT was better than that of group L-MT (Fig. 3). Thus recall was facilitated by originally higher muscular tension.(3) The after-effect of IMT on the following trials was studied with the performance of group T-N. In Exp. I, the after-effect of IMT was not found but in Exp. II it was shown up to 120 sec. after acquisition (Fig. 6).(4) The interaction between the effects of IMT and MT was not found (Fig. 1). However further studies are necessary to investigate into individual innate muscular tension and muscular tension generalized from IMT and other muscular movement.
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals (2023)

Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance mechanisms are often unknown. To reveal tolerance mechanisms, an automated platform was utilized to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals (1,2-propanediol, 2,3-butanediol, glutarate, adipate, putrescine, hexamethylenediamine, butanol, isobutyrate, coumarate, octanoate, hexanoate), reaching tolerance at concentrations 60%-400% higher than initial toxic levels. Sequencing genomes of 223 isolates from 89 populations, reverse engineering, and cross-compound tolerance profiling were employed to uncover tolerance mechanisms. We show that: 1) cells are tolerized via frequent mutation of membrane transporters or cell wall-associated proteins (e.g., ProV, KgtP, SapB, NagA, NagC, MreB), transcription and translation machineries (e.g., RpoA, RpoB, RpoC, RpsA, RpsG, NusA, Rho), stress signaling proteins (e.g., RelA, SspA, SpoT, YobF), and for certain chemicals, regulators and enzymes in metabolism (e.g., MetJ, NadR, GudD, PurT); 2) osmotic stress plays a significant role in tolerance when chemical concentrations exceed a general threshold and mutated genes frequently overlap with those enabling chemical tolerance in membrane transporters and cell wall-associated proteins; 3) tolerization to a specific chemical generally improves tolerance to structurally similar compounds whereas a tradeoff can occur on dissimilar chemicals, and 4) using pre-tolerized starting isolates can hugely enhance the subsequent production of chemicals when a production pathway is inserted in many, but not all, evolved tolerized host strains, underpinning the need for evolving multiple parallel populations. Taken as a whole, this study provides a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 223 chemical tolerant isolates.
Thermally Accelerated Oxidative Degradation of Quercetin Using Continuous Flow Kinetic Electrospray-Ion Trap-Time of Flight Mass Spectrometry (2013)

Thermally accelerated oxidative degradation of aqueous quercetin at pH 5.9 and 7.4 was kinetically measured using an in-house built online continuous flow device made of concentric capillary tubes, modified to fit to the inlet of an electrospray ionization-ion trap-time-of-flight-mass spectrometer (ESI-IT-TOF-MS). Time-resolved mass spectral measurements ranging from 2 to 21 min were performed in the negative mode to track intermediate degradation products and to evaluate the degradation rate of the deprotonated quercetin ion, [Q-H](-). Upon heating solutions in the presence of dissolved oxygen, degradation of [Q-H](-) was observed and was accelerated by an increase in pH and temperature. Regardless of the condition, the same degradation pathways were observed. Degradation mechanisms and structures were determined using higher order tandem mass spectrometry (up to MS(3)) and high mass accuracy. The observed degradation mechanisms included oxidation, hydroxylation, and ring-cleavage by nucleophilic attack. A chalcan-trione structure formed by C-ring opening after hydroxylation at C2 was believed to be a precursor for other degradation products, formed by hydroxylation at the C2, C3, and C4 carbons from attack by nucleophilic species. This resulted in A-type and B-type ions after cross-ring cleavage of the C-ring. Based on time of appearance and signal intensity, nucleophilic attack at C3 was the preferred degradation pathway, which generated 2,4,6-trihydroxymandelate and 2,4,6-trihydroxyphenylglyoxylate ions. Overall, 23 quercetin-related ions were observed.
[Benzidine and its derivatives in the immunohistochemical analysis of peroxidase]. (1989)

Authors have studied the application of benzidine and its derivatives for the demonstration of the marker enzyme horseradish peroxidase. Benzidine compounds are known to be in a blueish dimeric form under oxidative circumstances, while after polymerization they yield a dark brown end product. If the dimeric state is stabilized, the 3,3'-dimethoxy benzidine (o-dianisidin) appears to be the most suitable to demonstrate peroxidase. The o-dianisidin reaction has the advantage of high sensitivity and that the end product shows a birefringence in polarized light. Upon mounting with organic media the end product is stable.
Seizure suppression and neuroprotection by targeting the purinergic P2X7 receptor during status epilepticus in mice (2011)

Prolonged seizures [status epilepticus (SE)] constitute a neurological emergency that can permanently damage the brain. SE results from a failure of the normal mechanisms to terminate seizures; in particular, γ-amino butyric acid-mediated inhibition, and benzodiazepine anticonvulsants are often incompletely effective. ATP acts as a fast neurotransmitter via ionotropic ligand-gated P2X receptors. Here we report that SE induced by intra-amygdala kainic acid in mice selectively increased hippocampal levels of P2X7 receptors relative to other P2X receptors. Using transgenic P2X7 reporter mice expressing enhanced green fluorescent protein, we identify dentate granule neurons as the major cell population transcribing the P2X7 receptor after SE. Pretreatment of mice with an intracerebroventricular microinjection of 1.75 nmol A438079, a P2X7 receptor antagonist, reduced seizure duration by 58% and reduced seizure-induced neuronal death by 61%. Injection of brilliant blue G (1 pmol), another selective antagonist, reduced seizure duration by 48% and was also neuroprotective. A438079 was seizure-suppressive when injected shortly after induction of SE, and coinjection of A438079 with lorazepam 60 min after triggering SE, when electrographic seizure-responsiveness to lorazepam had decreased, also terminated SE. Our results suggest that P2X7 receptor antagonists may be a promising class of drug for seizure abrogation and neuroprotection in SE.
Characterization of a Novel Fibroblast Growth Factor 10 (Fgf10) Knock-In Mouse Line to Target Mesenchymal Progenitors during Embryonic Development (2012)

Fibroblast growth factor 10 (Fgf10) is a key regulator of diverse organogenetic programs during mouse development, particularly branching morphogenesis. Fgf10-null mice suffer from lung and limb agenesis as well as cecal and colonic atresia and are thus not viable. To date, the Mlcv1v-nLacZ-24 transgenic mouse strain (referred to as Fgf10(LacZ)), which carries a LacZ insertion 114 kb upstream of exon 1 of Fgf10 gene, has been the only strain to allow transient lineage tracing of Fgf10-positive cells. Here, we describe a novel Fgf10(Cre-ERT2) knock-in line (Fgf10(iCre)) in which a Cre-ERT2-IRES-YFP cassette has been introduced in frame with the ATG of exon 1 of Fgf10 gene. Our studies show that Cre-ERT2 insertion disrupts Fgf10 function. However, administration of tamoxifen to Fgf10(iCre); Tomato(flox) double transgenic embryos or adult mice results in specific labeling of Fgf10-positive cells, which can be lineage-traced temporally and spatially. Moreover, we show that the Fgf10(iCre) line can be used for conditional gene inactivation in an inducible fashion during early developmental stages. We also provide evidence that transcription factors located in the first intron of Fgf10 gene are critical for maintaining Fgf10 expression over time. Thus, the Fgf10(iCre) line should serve as a powerful tool to explore the functions of Fgf10 in a controlled and stage-specific manner.
Antiresonant Fabry-Perot quantum-well modulatortoactively modelock and synchronise solid-state lasers (1995)

The authors demonstrate active modelocking of an Nd:YLF laser using a semiconductor quantum-well reflectivity modulator as a cavity end mirror. The laser was modelocked at the fundamental frequency (100 MHz) and at harmonics up to 1.6 GHz. Synchronisation of passively modelocked pulses to an external RF signal was also demonstrated.
Going Green: The Role of the Green Tea Component EGCG in Chemoprevention (2013)

Tea is one of the most consumed beverages worldwide, and green tea is the least processed from the buds of the <i>Camellia sinensis</i> plant. The most abundant component of green tea is (-)-epigallocatechin-3-gallate (EGCG), which has been the focus of many cell culture, animal and clinical trials, revealing that EGCG possesses antiproliferative, antimutagenic, antioxidant, antibacterial, antiviral and chemopreventive effects. In this review we briefly summarize the mechanism of action(s) of the green tea component EGCG, highlighting recent advances in the epigenetic regulation by EGCG. Additionally, we provide an overview of mouse chemoprevention studies and EGCG chemoprevention clinical trials.
Decision-Tree, Rule-Based, and Random Forest Classification of High-Resolution Multispectral Imagery for Wetland Mapping and Inventory (2018)

Efforts are increasingly being made to classify the world's wetland resources, an important ecosystem and habitat that is diminishing in abundance. There are multiple remote sensing classification methods, including a suite of nonparametric classifiers such as decision-tree (DT), rule-based (RB), and random forest (RF). High-resolution satellite imagery can provide more specificity to the classified end product, and ancillary data layers such as the Normalized Difference Vegetation Index, and hydrogeomorphic layers such as distance-to-a-stream can be coupled to improve overall accuracy (OA) in wetland studies. In this paper, we contrast three nonparametric machine-learning algorithms (DT, RB, and RF) using a large field-based dataset (<i>n</i> = 228) from the Selenga River Delta of Lake Baikal, Russia. We also explore the use of ancillary data layers selected to improve OA, with a goal of providing end users with a recommended classifier to use and the most parsimonious suite of input parameters for classifying wetland-dominated landscapes. Though all classifiers appeared suitable, the RF classification outperformed both the DT and RB methods, achieving OA >81%. Including a texture metric (homogeneity) substantially improved the classification OA. However, including vegetation/soil/water metrics (based on WorldView-2 band combinations), hydrogeomorphic data layers, and elevation data layers to increase the descriptive content of the input parameters surprisingly did not markedly improve the OA. We conclude that, in most cases, RF should be the classifier of choice. The potential exception to this recommendation is under the circumstance where the end user requires narrative rules to best manage his or her resource. Though not useful in this study, continuously increasing satellite imagery resolution and band availability suggests the inclusion of ancillary contextual data layers such as soil metrics or elevation data, the granularity of which may define its utility in subsequent wetland classifications.
Prediction of Stone Composition from Plain Radiographs: A Prospective Study* (1999)

With a random sampling of plain radiographs, a panel of physicians specializing in stone disease correctly diagnosed the composition of renal calculi less than half of the time without being given clinical information.
MoSh (2014)

Marker-based motion capture (mocap) is widely criticized as producing lifeless animations. We argue that important information about body surface motion is present in standard marker sets but is lost in extracting a skeleton. We demonstrate a new approach called MoSh (Motion and Shape capture), that automatically extracts this detail from mocap data. MoSh estimates body shape and pose together using sparse marker data by exploiting a parametric model of the human body. In contrast to previous work, MoSh solves for the marker locations relative to the body and estimates accurate body shape directly from the markers without the use of 3D scans; this effectively turns a mocap system into an approximate body scanner. MoSh is able to capture soft tissue motions directly from markers by allowing body shape to vary over time. We evaluate the effect of different marker sets on pose and shape accuracy and propose a new sparse marker set for capturing soft-tissue motion. We illustrate MoSh by recovering body shape, pose, and soft-tissue motion from archival mocap data and using this to produce animations with subtlety and realism. We also show soft-tissue motion retargeting to new characters and show how to magnify the 3D deformations of soft tissue to create animations with appealing exaggerations.
Konrad Bloch, PhD (2011)

Konrad Bloch, PhD (1912–2000)



Konrad Bloch was born on January 21, 1912, in Neisse, the German province of Silesia, into a comfortable middle-class household. In 1941, Bloch married Lore Teutsch, originally from Munich, and they had 2 children, Peter and Susan. As a child, Bloch was interested in the natural sciences, and after completing secondary school, he enrolled in the University of Technology, Munich (the Technische Hochschule). Bloch enjoyed introductory courses in chemistry, particularly the organic chemistry course taught by Dr. Hans Fischer. Bloch’s opportunity to continue his graduate education in Germany studying chemistry was cut short by the rise of the Nazi party and their restrictions on people of Jewish descent. Fortunately, Fischer came to Bloch’s aid by referring him to Dr. Fredric Roulet, a pathologist and head of the Schweizerisches Hohenforschung Institut in Davos, Switzerland. Davos was famous for the longest ski runs in the Alps and for its many tuberculosis sanatoria. Under the supervision of Roulet, Bloch’s first research project was to determine the nature of the lipids found in Mycobacterium tuberculosis (M. tuberculosis) , with the hope that understanding the unique biochemistry of mycobacterial lipids would offer insight into the development of drugs to treat tuberculosis. A prior student in Roulet’s laboratory had identified cholesterol in M. tuberculosis , which was contrary to the finding by Chargaff in 1935 that cholesterol was absent in M. tuberculosis .1 Bloch’s first task was to repeat those studies. When he was unable to find cholesterol in M. tuberculosis , Roulet was displeased that the results of his previous student could not be repeated.1 However, when similar negative findings were reported by R.J. Anderson and R. Schoenheimer from Columbia University in New York City, Roulet accepted his work.

Bloch moved on to investigate the phospholipid chemistry of M. …
A novel urinary sialoglycoprotein as the inhibitor of interleukin-1. (1989)

An inhibitor of interleukin-1 (IL-1) was purified to homogeneity from febrile human urine by using a sequence of ammonium sulphate fractionation, DEAE-cellulose chromatography and gel filtration on a column of ACA 54. The inhibitor was a sialoglycoprotein and its molecular weight, examined by SDS-PAGE, was found to be 30 kD. It was acidic in nature and its isoelectric point, determined by electrofocusing on thin-layer polyacrylamide gels, was found to be 3.5-3.6. The inhibitor was sensitive to the action of sialidase from Vibrio cholerae as the enzyme treated material was electrofocused at a higher pH range (4.5-5.2). The inhibitor contained 10% sialic acid as estimated by the Thiobarbituric acid assay. It interacted with the lectins jacalin and concanavalin A, suggesting the presence of carbohydrate moieties such as galactose and mannose. The inhibitor did not block the specific binding of IL-1 to cells, nor did it directly bind IL-1. Early rejection urine from a kidney transplant patient was also found to contain the 30 kD IL-1 inhibitor protein. This was visualised by immunoblotting using specific antibody raised against the 30 kD IL-1 inhibitor isolated from the urine of febrile patients.