gebhart/patrepeval huggingface dataset:
Cytomegalovirus Kinetics Following Primary Infection in Healthy Women (2017)

The kinetics of cytomegalovirus (CMV) DNA in infected asymptomatic hosts are largely unknown. We measured viral load (VL) in 124 fluid samples (oral, urine, vaginal, blood) collected from 21 women who acquired CMV. A quantitative real-time polymerase chain reaction assay of US17, which correlated with clinical assays, was used. VL decreased following primary infection in all fluids. The geometric mean VL of vaginal fluid was significantly higher than that of other sources: oral (3.89; 95% confidence interval [CI], 1.43-10.57), urine (6.36; 95% CI, 2.48-16.32), and whole blood (11.88; 95% CI, 4.12-34.20). Vaginal CMV shedding may provide a route for sexual and possibly perinatal transmission.
Identification of Intramembrane Particles by Pre- and Post-Fracture Labelling Techniques: A Progress Report (1980)

Conventional freeze-fracture replicas provide for high resolution, three-dimensional replication of the internal macromolecular architecture of cell membranes, but they have the distinct disadvantage that no biologically rele¬vant macromolecules remain for subsequent in situ labelling and positive identification. Recently, several ingenious freeze-fracture techniques have been devised to localize biochemical components before the tissues are diges-ted away. These methods include (a) freeze-fracture autoradiography of the frozen whole mount preparation (1, 2) and (b) deep etching (freeze-drying) to expose immunoglobins or other large protein markers attached to membrane surfaces (3). However, freeze-fracture autoradiography has insufficient resolution to permit localization of labels to individual intramembrane particles (IMPs) exposed by the cleaving process, while deep etching to reveal membrane surfaces does not reveal IMPs. To overcome some of these difficulties, we recently introduced the "sectioned replica technique" to provide a method for direct and unambiguous correlation of freeze-fracture and thin section images within a single electron micrograph (4). The fractured and replicated tissues are thawed, but instead of digesting the tissues, the replica-tissue sandwich is post-fixed in 30% buffered glycerol solution con-taining 1% OsO 4 , post-stained, embedded in plastic, and sectioned parallel to the replica-tissue interface. Using this sectioned-replica technique, we have been able to obtain (a) pre-fracture radioisotope-labelled mouse neuromuscular junctions and (b) pre- and post-fracture immunoferritin and colloidal gold-labelled membrane fragments and intact neuromuscular junctions.
RETRACTED: Cdx2 Gene Expression and Trophectoderm Lineage Specification in Mouse Embryos (2006)

Controversy exists as to whether individual blastomeres from two-cell-stage mouse embryos have identical developmental properties and fate. We show that the transcription factor Cdx2 is expressed in the nuclei of cells derived from the late-dividing but not the first-dividing blastomere of two-cell embryos and, by lineage tracing and RNA interference knock-down experiments, that this lagging cell is the precursor of trophectoderm. Cdx2 mRNA is localized toward the vegetal pole of oocytes, reorients after fertilization, and becomes concentrated in the late-dividing, two-cell-stage blastomere. The asymmetrical distribution of Cdx2 gene products in the oocyte and embryo defines the lineage to trophectoderm.
Arginine catabolic mobile element encoded speG abrogates the unique hypersensitivity of Staphylococcus aureus to exogenous polyamines (2011)

Polyamines, including spermine (Spm) and spermidine (Spd), are aliphatic cations that are reportedly synthesized by all living organisms. They exert pleiotropic effects on cells and are required for efficient nucleic acid and protein synthesis. Here, we report that the human pathogen Staphylococcus aureus lacks identifiable polyamine biosynthetic genes, and consequently produces no Spm/Spd or their precursor compounds putrescine and agmatine. Moreover, while supplementing defined medium with polyamines generally enhances bacterial growth, Spm and Spd exert bactericidal effects on S. aureus at physiological concentrations. Small colony variants specifically lacking menaquinone biosynthesis arose after prolonged Spm exposure and exhibited reduced polyamine sensitivity. However, other respiratory-defective mutants were no less susceptible to Spm implying menaquinone itself rather than general respiration is required for full Spm toxicity. Polyamine hypersensitivity distinguishes S. aureus from other bacteria and is exhibited by all tested strains save those belonging to the USA-300 group of community-associated methicillin-resistant S. aureus (CA-MRSA). We identified one gene within the USA-300-specific arginine catabolic mobile element (ACME) encoding a Spm/Spd N-acetyltransferase that is necessary and sufficient for polyamine resistance. S. aureus encounters significant polyamine levels during infection; however, the acquisition of ACME encoded speG allows USA-300 clones to circumvent polyamine hypersensitivity, a peculiar trait of S. aureus.
Behavioral responses of Escherichia coli to changes in redox potential. (1996)

Escherichia coli bacteria sensed the redox state in their surroundings and they swam to a niche that had a preferred reduction potential. In a spatial redox gradient of benzoquinone/benzoquinol, E. coli cells migrated to form a sharply defined band. Bacteria swimming out of either face of the band tumbled and returned to the preferred conditions at the site of the band. This behavioral response was named redox taxis. Redox molecules, such as substituted quinones, that elicited redox taxis, interact with the bacterial electron transport system, thereby altering electron transport and the proton motive force. The magnitude of the behavioral response was dependent on the reduction potential of the chemoeffector. The Tsr, Tar, Trg, Tap, and CheR proteins, which have a role in chemotaxis, were not essential for redox taxis. A cheB mutant had inverted responses in redox taxis, as previously demonstrated in aerotaxis. A model is proposed in which a redox effector molecule perturbs the electron transport system, and an unknown sensor in the membrane detects changes in the proton motive force or the redox status of the electron transport system, and transduces this information into a signal that regulates phosphorylation of the CheA protein. A similar mechanism has been proposed for aerotaxis. Redox taxis may play an important role in the distribution of bacterial species in natural environments.
Synthesis of the First Penicillin Derivatives with Medium‐Sized Lactam Ring and of Related Thiazolidines (1995)

Abstract The novel concept of penicillin derivatives 4 with a medium‐sized instead of a β‐lactam ring is presented. Two synthetic paths were invented, resulting in the evaluation of the synthetic potential in the succinic, glutaric, and adipic acid series. A number of novel penicillin‐derived thiazolidines were prepared, notably the derivatives 16 and 22 with anellated 7‐ and 13‐membered lactam ring.
A Kidney‐targeted Protein Biopolymer Drug Delivery System (2015)

Elastin-like Polypeptides (ELPs) are bioengineered protein polymers that can be used as drug carriers. ELPs are composed of a repeating pentapeptide motif, their sequence is genetically encoded, and they are produced by recombinant expression in E. coli. Simple molecular biology strategies are used to change the number of pentapeptide repeats to tune the polymer's size and to modify the sequence's N- and C-termini to add targeting peptides and therapeutic peptides, therapeutic proteins, or reactive sites for drug conjugation. In addition to its amenability to sequence modification, ELP is a thermally responsive biopolymer. It self-associates into aggregates above a user defined transition temperature, and the aggregation process is fully reversible. This allows ELP and ELP-fusion proteins to be purified using simple thermal precipitation. We previously showed that ELP has a high affinity for the kidney when administered by systemic injection. Here, we assessed the ability of targeting peptides to increase the kidney binding and kidney specificity. Two non-organ specific cell penetrating peptides (Tat and SynB1) and one renal-specific kidney targeting peptide (KTP) were fused to ELP, and their pharmacokinetics and biodistribution were determined using quantitative fluorescence measurements in a rat model. All three peptides increased kidney deposition of ELP by over four-fold (p < 0.0001), but the KTP was the most specific for the kidney, achieving targeting levels of 15-fold when comparing kidney:liver ratios and 150-fold when comparing kidney:heart ratios. This research was supported by NIH grant R01HL121527 to GLB and NIH grant R01HL095638 and AHA grant 18490005 to ARC.
Electromagnetic modeling of non-uniform through-silicon via (TSV) interconnections (2012)

In this paper, a hybrid approach for electromagnetic modeling of complex tapered through-silicon via (TSV) in three dimensional integrated circuits (3D ICs) is proposed. For complex TSV structures, TSVs are divided vertically into conical and cylindrical sections. The modeling of conical TSV is presented based on using conical modal basis functions. By using the conical TSV modeling method combined with cylindrical TSV modeling method, complex TSV structures can be modeled efficiently. The accuracy of this hybrid method is validated by comparison with 3-D full-wave simulations.
Minerals and Cancer: Overview of the Possible Diagnostic Value (2022)

Cancer is the second leading cause of death worldwide and is expected to increase by one-third over the next two decades, in parallel with the growing proportion of the elderly population. Treatment and control of cancer incidence is a global issue. Since there is no clear way to prevent or cure this deadly malignancy, diagnostic, predictive, and prognostic markers for oncological diseases are of great therapeutic value. Minerals and trace elements are important micronutrients for normal physiological function of the body. They are abundant in natural food sources and are regularly included in dietary supplements whereas highly processed industrial food often contains reduced or altered amounts of them. In modern society, the daily intake, storage pools, and homeostasis of these micronutrients are dependent on certain dietary habits and can be thrown out of balance by malignancies. The current work summarizes the data on minerals and trace elements associated with abnormal accumulation or depletion states in tumor patients and discusses their value as potential tumor-associated biomarkers that could be introduced into cancer therapy.
Carbon Capture and Storage: How Green Can Black Be? (2009)

The capture of carbon dioxide at the point of emission from coal- or gas-burning power plants is an attractive route to reducing carbon dioxide emissions into the atmosphere. To commercialize carbon capture, as well as transport of liquified carbon dioxide and its storage in exploited oil fields or saline formations, many technological, commercial, and political hurdles remain to be overcome. Urgent action is required if carbon capture and storage is to play a large role in limiting climate change.
Epoxy resin modified by aliphatic cyclic carbonates (1990)

Abstract Bidentate and tridentate cyclic carbonates obtained from the reaction of aliphatic epoxy compounds with carbon dioxide were used for the modification of an epoxy resin. The compositions obtained exhibited low viscosity, short gel time, and low exothermic effect accompanying the crosslinking. On the basis of model reactions, a mutually accelerating effect of epoxy and cyclic carbonate groups on the crosslinking of the studied systems by triethylenetetramine was found (synergistic effect). The cured epoxide–cyclic carbonate compositions exhibited considerably higher impact resistance and tensile strength in comparsion with epoxy resins.
IMAGING DIAGNOSIS—BILATERAL ORTHOTOPIC URETEROCELES IN A DOG (2011)

A 5-year-old neutered male Akita had a 5-month history of hematuria. Bilateral orthotopic ureteroceles were diagnosed using a combination of sonography, computed tomography (CT), and radiography. With CT excretory urography, the ureteroceles appeared as two intraluminal cystic structures in the vesicoureteral region of the urinary bladder, which directly communicated with dilated ureters. Unlike the other imaging modalities CT excretory urography provided a definitive diagnosis by confirming the communication between the hydroureters and the cystic dilations in the caudodorsal aspect of the urinary bladder.
Hydrofocusing Bioreactor for Three-Dimensional Cell Culture (2003)

The hydrodynamic focusing bioreactor (HFB) is a bioreactor system designed for three-dimensional cell culture and tissue-engineering investigations on orbiting spacecraft and in laboratories on Earth. The HFB offers a unique hydrofocusing capability that enables the creation of a low-shear culture environment simultaneously with the herding of suspended cells, tissue assemblies, and air bubbles. Under development for use in the Biotechnology Facility on the International Space Station, the HFB has successfully grown large three-dimensional, tissuelike assemblies from anchorage-dependent cells and grown suspension hybridoma cells to high densities. The HFB, based on the principle of hydrodynamic focusing, provides the capability to control the movement of air bubbles and removes them from the bioreactor without degrading the low-shear culture environment or the suspended three-dimensional tissue assemblies. The HFB also provides unparalleled control over the locations of cells and tissues within its bioreactor vessel during operation and sampling.
Visualizing earthwork and information on a linear infrastructure project using BIM 4D (2018)

Countries worldwide are facing the need for infrastructure improvements on a large scale. Projects concerning road, railway, tunnel and pipelines include a large amount of earthworks which is often delayed or has considerable cost overruns. This study presents a method to assist earthwork planning, by extracting separate 3D objects of cutting and filling, attaching schedule information and visualize these in commercial BIM 4D software. The 4D method was applied and verified in the re-scheduling of a linear infrastructure project which is one of the German governments selected pilot projects before implementing BIM requirements in 2020.The study indicated that the 4D visualization enable information flow between projects participants. The paper gives suggestions to the level of information detailing standardized open data format should be able to contain in regards of facilitating the use of BIM 4D information visualizing in future linear infrastructure projects.
Three-Dimensional Whole-Brain Mapping (1992)

The implementation and use of a computerized whole-brain mapping system which can be used in conjunction with MRI, CT, angiographic and other brain imaging techniques is described. Three mapping systems based upon common reference structures about the third and fourth ventricular core of the brain are used in conjunction with internationally recognized nomenclature to create a normalized whole-brain mapping system according to the Talairach/Tournoux proportional grid technique.
A novel fully human antitumor ImmunoRNase resistant to the RNase inhibitor (2012)

The ErbB2 tyrosine kinase receptor is an attractive target for immunotherapy, as it is overexpressed in many carcinomas. ImmunoRNases, made up of a human anti-ErbB2 scFv (single chain antibody fragment) and human RNases, have been engineered to overcome the limits of immunotoxins, made up of mouse antibodies and plant or bacterial toxins, such as immunogenicity and non-specific toxicity. Here we describe the construction and characterization of a second-generation anti-ErbB2 immunoRNase, called ERB-HP-DDADD-RNase, obtained by fusing Erbicin, a human ErbB2-directed scFv, with an inhibitor-resistant variant of human pancreatic RNase (HP-DDADD-RNase). This novel immunoRNase retains both the enzymatic activity of human pancreatic RNase and the specific binding of the parental scFv to ErbB2-positive cells, showing an affinity comparable with that of the previously reported parental immunoRNase (ERB-HP-RNase). Moreover, the novel immunoRNase is endowed with an effective and selective in vitro antiproliferative action for ErbB2-positive tumor cells, which is more potent than that of the parental immunoRNase on tumor cells expressing low levels of ErbB2, due to its resistance to the RNase inhibitor. Thus, the novel immunoRNase could represent a valuable tool for ErbB2-positive cancer therapy.
Determining thresholds for spatial urban design and transport features that support walking to create healthy and sustainable cities: findings from the IPEN Adult study (2022)

An essential characteristic of a healthy and sustainable city is a physically active population. Effective policies for healthy and sustainable cities require evidence-informed quantitative targets. We aimed to identify the minimum thresholds for urban design and transport features associated with two physical activity criteria: at least 80% probability of engaging in any walking for transport and WHO's target of at least 15% relative reduction in insufficient physical activity through walking. The International Physical Activity and the Environment Network Adult (known as IPEN) study (N=11 615; 14 cities across ten countries) provided data on local urban design and transport features linked to walking. Associations of these features with the probability of engaging in any walking for transport and sufficient physical activity (≥150 min/week) by walking were estimated, and thresholds associated with the physical activity criteria were determined. Curvilinear associations of population, street intersection, and public transport densities with walking were found. Neighbourhoods exceeding around 5700 people per km<sup>2</sup>, 100 intersections per km<sup>2</sup>, and 25 public transport stops per km<sup>2</sup> were associated with meeting one or both physical activity criteria. Shorter distances to the nearest park were associated with more physical activity. We use the results to suggest specific target values for each feature as benchmarks for progression towards creating healthy and sustainable cities.
New quinolone antibiotics: a survey of the literature from 2005 to 2010 (2010)

Despite nearly 40 years of research, quinolones still provide new analogs of both scientific and clinical interest. Compounds that are active against antibiotic resistant strains including multiple drug-resistant Mycobacterium tuberculosis as well as compounds with improved pharmacokinetic and safety profiles are goals for current and future programs in this area.
Minimum-Cost Network Design with (Dis)economies of Scale (2010)

Given a network, a set of demands and a cost function f(.), the min-cost network design problem is to route all demands with the objective of minimizing Σ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> f(ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> ), where ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> is the total traffic load under the routing. We focus on cost functions of the form f(x) = σ + x <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">α</sup> for x > 0, with f(0) = 0. For α ≤ 1 f(.) is subadditive and exhibits behavior consistent with economies of scale. This problem corresponds to the well-studied Buy-at-Bulk network design problem and admits polylogarithmic approximation and hardness. In this paper, we focus on the less studied scenario of α > 1 with a positive startup cost σ > 0. Now, the cost function f(.) is neither subadditive nor superadditive. This is motivated by minimizing network-wide energy consumption when supporting a set of traffic demands. It is commonly accepted that, for some computing and communication devices, doubling processing speed more than doubles the energy consumption. Hence, in Economics parlance, such a cost function reflects diseconomies of scale. We begin by discussing why existing routing techniques such as randomized rounding and tree-metric embedding fail to generalize directly. We then present our main contribution, which is a polylogarithmic approximation algorithm. We obtain this result by first deriving a bicriteria approximation for a related capacitated min-cost flow problem that we believe is interesting in its own right. Our approach for this problem builds upon the well-linked decomposition due to Chekuri-Khanna-Shepherd, the construction of expanders via matchings due to KhandekarRao-Vazirani, and edge-disjoint routing in well-connected graphs due to Rao-Zhou. However, we also develop new techniques that allow us to keep a handle on the total cost, which was not a concern in the aforementioned literature.
Catheter ablation of left ventricle summit PVC using anterior interventricular vein approach (2022)

A young female patient with normal ejection fraction. History of premature ventricular complex (PVC) radiofrequency ablation located in left ventricular outflow tract. Two years later frequent PVC is observed in a different location (> 47000 in 24 h Holter). Anti-arrhythmic drugs were used unsuccessfully. PVCs were located in left ventricular summit. Radiofrequency ablation through coronary sinus and anterior interventricular vein was performed. During follow-up, no recurrence was observed.
A 0.5-V 8-bit 10-Ms/s Pipelined ADC in 90-nm CMOS (2008)

This paper presents a pipelined analog-to-digital converter (ADC) operating from a 0.5-V supply voltage. The ADC uses true low-voltage design techniques that do not require any on-chip supply or clock voltage boosting. The switch OFF leakage in the sampling circuit is suppressed using a cascaded sampling technique. A front-end signal-path sample-and-hold amplifier (SHA) is avoided by using a coarse auxiliary sample and hold (S/H) for the sub-ADC and by synchronizing the sub-ADC and pipeline-stage sampling circuit. A 0.5-V operational transconductance amplifier (OTA) is presented that provides inter-stage amplification with an 8-bit performance for the pipelined ADC operating at 10 Ms/s. The chip was fabricated on a standard 90 nm CMOS technology and measures 1.2 mm times 1.2 mm. The prototype chip has eight identical stages and stage scaling was not used. It consumes 2.4 mW for 10-Ms/s operation. Measured peak SNDR is 48.1 dB and peak SFDR is 57.2 dB for a full-scale sinusoidal input. Maximal integral nonlinearity and differential nonlinearity are 1.19 and 0.55 LSB, respectively.
Oncogenic Drivers and Development (2019)

In this issue of <i>Cancer Discovery</i>, Lopez and colleagues show that the aggressive acute leukemic phenotype caused by the chimeric transcription factor CBFA2T3-GLIS2 varies depending on the developmental stage of the cell transformed (i.e., fetal vs. adult). This is likely a general principle in pediatric cancers and begins to explain why some cancer phenotypes are more common in infants and young children, whereas others are more frequent in older individuals.<i>See related article by Lopez et al., p. 1736</i>.