gebhart/patrepeval huggingface dataset:
One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9 (2016)

Abstract Bacteria are indispensable for the study of fundamental molecular biology processes due to their relatively simple gene and genome architecture. The ability to engineer bacterial chromosomes is quintessential for understanding gene functions. Here we demonstrate the engineering of the small-ribosomal subunit (16S) RNA of Mycoplasma mycoides , by combining the CRISPR/Cas9 system and the yeast recombination machinery. We cloned the entire genome of M. mycoides in yeast and used constitutively expressed Cas9 together with in vitro transcribed guide-RNAs to introduce engineered 16S rRNA genes. By testing the function of the engineered 16S rRNA genes through genome transplantation, we observed surprising resilience of this gene to addition of genetic elements or helix substitutions with phylogenetically-distant bacteria. While this system could be further used to study the function of the 16S rRNA, one could envision the “simple” M. mycoides genome being used in this setting to study other genetic structures and functions to answer fundamental questions of life.
Advances in the Knowledge and Clinical Applications of Lactic Acid Bacteria as Probiotics in the Urogenital Tract (2008)

Probiotics, defined as live microorganisms administered in high numbers to produce beneficial and physiological effects on the host, are increasingly applied to the prevention and treatment of many clinical situations in both human beings and animals. The female urogenital tract is one of the targets of probiotics, mainly by the frequency of infectious diseases that affects patients of all ages, including pregnant women and, potentially, newborns. Urogenital infections are associated with high morbidity and mortality rates as well as with high health care costs. The development of a probiotic formula to control these situations is of great interest. In this review, the mechanisms that support the probiotic action of lactic acid bacteria in the urogenital tract are summarized. Animal models used to test their effect on certain pathologies as well as clinical trials performed in humans are described. Some products currently available on the market are also mentioned. Keywords: Lactic acid bacteria, urogenital tract, probiotics, in vivo assays, clinical trials
Natural History of Cone Disease in the Murine Model of Leber Congenital Amaurosis Due to CEP290 Mutation: Determining the Timing and Expectation of Therapy (2014)

The natural history of early loss of photoreceptor function with retained cone cell nuclei is common to both CEP290-LCA patients and the rd16;Nrl-/- murine model. Pre-clinical proof-of-concept studies for uniocular therapies would seem most appropriate to begin with intervention at P35-40 and re-study after one month by assaying interocular difference in the UV-cone ERG.
Rapid sexing of human embryos by non‐radioactive in situ hybridization: Potential for preimplantation diagnosis of X‐linked disorders (1989)

Sixty spare human embryos at various stages of preimplantation development were prepared for cytogenetic analysis. Fluorescent staining of those with metaphases allowed scoring for the presence of a Y chromosome. In situ hybridization was then performed using a biotinylated Y-specific sequence, and the probe was detected by a standard streptavidin-linked alkaline phosphatase system. This enabled comparison of the chromosomal sex with that obtained after in situ hybridization in 28 embryos, and the sexing result obtained by the two methods was concordant in all cases. A further 21 embryos in which no metaphase chromosomes were obtained were sexed by biotinylated in situ hybridization only. Overall, 66 per cent of male interphase nuclei demonstrated a Y-specific hybridization signal. Results were obtained in under 24 h, which may permit the sexing of an embryo biopsied during cleavage and the transfer of sexed embryos at the blastocyst stage to the mother's uterus in the same cycle as oocytes are collected for in vitro fertilization.
Sub-threshold operation of a timing error detection latch (2009)

Significant demand for utlra-low power applications has provided an advantage for circuits capable of sub-threshold operation. The reduction of the supply voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> ) below the threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) of transistors, or sub-threshold, provides minimum energy consumption in digital CMOS logic. The exponential dependence of the drain current on V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> variations leads to increased overdesign if sub-threshold circuits are to be robust. One solution to variability robustness is timing error detection (TED). Presented here is a TED latch capable of subthreshold operation. It was designed in 65 nm CMOS, has an operating voltage range of 0.2 V through 1.2 V, and a minimum energy point (MEP) of 0.4 V. At the MEP, the average power consumption for one clock period and an activity factor of alpha=0.5 is 0.37 nW. The area of the TED latch is 93 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Identification of a peptide mimic of the L2/HNK‐1 carbohydrate epitope (2002)

The L2/HNK-1 carbohydrate is carried by many neural recognition molecules and is involved in neural cell interactions during development, regeneration in the peripheral nervous system, synaptic plasticity, and autoimmune-based neuropathies. Its key structure consists of a sulfated glucuronic acid linked to lactosaminyl residues. Because of its biological importance but limited availability, the phage display method was used to isolate a collection of peptide mimics that bind specifically to an L2/HNK-1 antibody. The phages isolated from a 15-mer peptide library by adsorption to this antibody share a consensus sequence of amino acids. The peptide mimicked several important functions of the L2/HNK-1 carbohydrate, such as binding to motor neurons in vitro, and preferential promotion of in vitro neurite outgrowth from motor axons compared with sensory neurons. A scrambled version of the peptide had no activity. The combined observations indicate that we have isolated a mimic of the L2/HNK-1 carbohydrate that is able to act as its functional substitute.
Chirurgische Maßnahmen bei kongenitalem Glaukom (1993)

An overview about the classification, diagnostic and therapy of congenital glaucomas is given. Tonometry, gonioscopy, corneal diameter measurements, oculometry and the evaluation of the optic disc are the main diagnostic criteria. Goniotomy is the operation of choice. The technique of goniotomy and their modifications leading to cyclodialysis ab interno are described. Own long-term results of goniotomy are finally demonstrated.
DFR: A New Improved Algorithm for Mining Frequent Itemsets (2007)

Efficiency has been concerned in the research of association rules mining. This paper presents an improved method called Direct-Fined-Remove (DFR) algorithm to mine a database consisting of remove and direct steps. When pruning the candidates itemsets, the algorithm eliminate non-frequent subset of candidates in the remove steps. In the direct steps, the algorithm directly generates the frequent itemsets by computing and comparing the frequency of frequent k-itemsts with k in the meantime. The contributions include: (1) proposes an algorithm to raise the probability of obtaining information in scanning database and reduce the potential scale of itemsets. (2) successfully applies the proposed algorithm to the Teaching Evaluation System to determine characteristics of good teaching effect. Experiments show that the probability which grade point of associate professor being more than 90 is 35% the support degree is 40% and the probability which grade point of bachelor being more than 90 is 16% the support degree is 83%.
Newborn hearing screening protocol in tuscany region (2017)

In the paper we report the modality of execution of the universal newborn hearing screening in the Tuscany Region, according to the recently updated protocol. The main features of the protocol and the critical issues are discussed.
PREDICTING THE EFFECTS OF FREEZING AND THAWING ON PAVEMENT SUPPORT (1998)

The objective of this study was to develop a method to predict the timing of weight limits on secondary highways in Wisconsin. Two types of weight limits are of interest: overloads when the pavement is frozen and weight restrictions during thawing and post-thawing recovery period. To meet this objective, three sections of secondary highways with flexible pavements were instrumented and monitored to determine how freezing, thawing, and post-thaw recovery affect pavement stiffness. Data collected from these sites were used to develop a computer model (UWFrost) that can be used to predict seasonal changes in the support capacity of pavements. The computer model is operated from a Microsoft Excel spreadsheet. Freezing and thawing were found to have a significant effect on the stiffness and capacity of flexible pavements. The pavement stiffens during winter when the base freezes, and softens substantially when the base and subgrade thaw. A gradual recovery process occurs after thawing is complete during which the pavement stiffens. This recovery process extends through a non-dimensional modulus ratio function that varies with time. This function is an intrinsic component of UWFrost. UWFrost simulates how freezing and thawing affect the stiffness and capacity of pavements. The user enters meteorological data, pavement location, pavement layer geometry, and timing criteria. A one-dimensional heat transfer module uses the input to define the moduli of the pavement layers, which are used in a layered elastic analysis. The elastic analysis is used iteratively to determine the load that induces no more damage than a design load applied during late summer. This load is referred to as the equivalent damage load (EDL). EDLs are defined for fatigue and rutting damage. UWFrost computes EDLs for each day during the prediction period selected by the user. EDLs are as much as three times higher than design loads when the base and subgrade are frozen. At the end of thaw, when the pavement reaches its softest condition, the EDL can be less than one-half the design load.
Crystallization and preliminary crystallographic analysis of the NAD(H)-binding domain ofEscherichia colitranshydrogenase (2004)

Transhydrogenase is a proton-pumping membrane protein that is required for the cellular regeneration of NADPH. The NAD(H)-binding domain (domain I) of transhydrogenase from Escherichia coli was crystallized using the hanging-drop vapour-diffusion technique at room temperature. The crystals, which were grown from PEG 4000 and ammonium acetate in citrate buffer, belong to the triclinic space group P1, with unit-cell parameters a = 38.8, b = 66.8, c = 76.4 A, alpha = 67.5, beta = 80.8, gamma = 81.5 degrees. X-ray diffraction data were collected to 1.9 A resolution using synchrotron radiation. The crystals contain one dimer of transhydrogenase domain I per asymmetric unit.
Computers help keep patient files confidential. (1990)

File folders stuffed with papers documenting a patient's hospital stay can be an administrative nightmare. Such medical records are easily misplaced and might already be checked out when they need to be reviewed. In addition, because so many eyes glance at such files, confidentiality is a problem. That's why some hospitals are purchasing information systems for their medical records departments.
Albumin labeled with Gd-DTPA as an intravascular, blood pool-enhancing agent for MR imaging: biodistribution and imaging studies. (1987)

Albumin is a macromolecule that remains largely confined to the vascular space after intravenous administration. Human serum albumin was paramagnetically labeled by covalently binding from nine to 18 gadolinium-DTPA (diethylenetriaminepentaacetic acid) chelates per protein molecule. This conjugate was tested in varying doses for in vivo biodistribution and effectiveness in tissue relaxation. After intravenous injection of the agent in rats, T1 relaxation times were significantly reduced in samples of the blood and in lung, heart, spleen, kidney, and brain tissue. These effects persisted at a relatively constant level for the next 30 minutes. In vivo magnetic resonance imaging of the heart and lungs of rats and rabbits confirmed the prolonged contrast-enhancing effect of the labeled albumin. These preliminary studies indicate that paramagnetically labeled macromolecules that distribute in the intravascular space may be effective for MR imaging evaluation of tissue blood volume.
Heating and structural disordering effects of the nonlinear viscous flow in a Zr55Al10Ni5Cu30 bulk metallic glass (2003)

The heat evolution of stress-induced structural disorder, ΔHs(ε), of a Zr55Al10Ni5Cu30 bulk metallic glass (BMG) during compressive constant ram-velocity deformation at the glass transition region (Tg=680 K) was deduced from in situ measurements of temperature change of the deforming sample. At the transition from the linear to nonlinear viscoelasticity, the behavior of viscosity change with strain, η(ε), is qualitatively consistent with the enthalpy evolution of the structural disordering, ΔHs(ε), but not with the temperature change, ΔT(ε). It is concluded that the initial softening deformation is due to the stress-induced structural disordering. The change in the nonlinearity, −log η̃ ≡−log η /ηN, is found to be proportional to the ΔHs and the slope of ΔHs(−log η̃) can be estimated to 400 J/mol, where ηN is the Newtonian viscosity. On the other hand, the temperature raise, ΔT(ε), is pronouncedly delayed as compared with the η (ε) and ΔHs(ε) at the transition, but is determined by a product of stress and plastic strain-rate, σ⋅ε̇p, and is nearly proportional to it at the steady state. The slope of ΔT(σ⋅ε̇p) can be estimated to 5.2×10−2 K mol/W.
Robust Ultramicroporous Metal–Organic Frameworks with Benchmark Affinity for Acetylene (2018)

Highly selective separation and/or purification of acetylene from various gas mixtures is a relevant and difficult challenge that currently requires costly and energy-intensive chemisorption processes. Two ultramicroporous metal-organic framework physisorbents, NKMOF-1-M (M=Cu or Ni), offer high hydrolytic stability and benchmark selectivity towards acetylene versus several gases at ambient temperature. The performance of NKMOF-1-M is attributed to their exceptional acetylene binding affinity as revealed by modelling and several experimental studies: in situ single-crystal X-ray diffraction, FTIR, and gas mixture breakthrough tests. NKMOF-1-M exhibit better low-pressure uptake than existing physisorbents and possesses the highest selectivities yet reported for C<sub>2</sub> H<sub>2</sub> /CO<sub>2</sub> and C<sub>2</sub> H<sub>2</sub> /CH<sub>4</sub> . The performance of NKMOF-1-M is not driven by the same mechanism as current benchmark physisorbents that rely on pore walls lined by inorganic anions.
A Validation Study of a Kinect Based Body Imaging (KBI) Device System Based on ISO 20685:2010 (2014)

To replace the traditional anthropometric data collection processes with the 3D acquiring system it is important that the validity of the data is not compromised. To do this, a validation study, based on the guideline of ISO 20685, can be performed. This paper presents the results of a comparison between traditional measurements and measurements taken with a 3D acquiring system using only four Kinect sensors. The results obtained were then compared with the maximum allowable error indicated in ISO 20685, concluding that this system cannot give sufficiently reliable data that can substitute the manual procedures.
Geometric Tumor Embolic Budding Characterizes Inflammatory Breast Cancer (2022)

Abstract Background The sina qua non of IBC is numerous tumor emboli especially within dermal lymphatics. The explanation remains a mystery. Methods In observational human studies comparing IBC with non-IBC, although common tumor parameters such as Ki-67 index, mitotic count and nuclear size showed a reasonable overlap, there was a dramatic exponential or geometric difference in embolic density and a significant difference in embolic size distribution in IBC v non-IBC. In companion experimental studies using contrasting properties of two xenografts, Mary-X and Karen-X, both derived from IBC patients, this study offers a novel explanation and mechanism to explain the high tumor embolic numbers in IBC. Results The explanation is geometric embolic budding. Mary-X exhibits florid lymphovascular tumor emboli in vivo which give rise to high numbers of CTCs and pulmonary metastases whereas Karen-X lacks these features. Mary-X also gives rise to tight spheroids in vitro which exhibit dynamic budding whereas Karen-X exhibits only loose non-budding aggregates. Furthermore Mary-X emboli also bud dramatically into daughter emboli in vivo . The mechanism that regulates the compactness of the spheroids as well as the emboli involves the generation of E-cad/NTF1, a calpain-mediated cleavage product of membrane E-cadherin. Inhibiting the generation of E-cad/NFT1 by blocking either the calpain site of cleavage (SC) or the site of binding (SB) with specific decapeptides both reduces spheroid compactness and decreases budding. Conclusions Since E-cad/NFT1 retains the p120ctn binding site but loses both the β-catenin and α-binding sites, promoting its 360° distribution around the cell’s membrane, the varying levels of expression of this truncated molecule may trigger budding of both the spheroids as well as the emboli. Recurrent and geometric budding of parental emboli into daughter emboli then would account for the plethora of tumor emboli seen in IBC patients.
Model to predict motion sickness within autonomous vehicles (2019)

Background: Motion sickness is common within most forms of transport; it affects most of the population who experience varied symptoms at some stage in their lives. Thus far, there has been no specific method to quantify the predicted levels of motion sickness for a given vehicle design, task and route. Objective: To develop a motion sickness virtual prediction tool that includes the following inputs: human motion, vision, vehicle motion, occupant task and vehicle design. Method: A time domain analysis using a multi-body systems approach has been developed to provide the raw data for post-processing of vehicle motion, occupant motion and vision, based on a virtual route designed to provoke motion sickness, while the digital occupant undertakes a specific non-driving related task. Results: Predicted motion sickness levels are shared for a simple positional sweep of a vehicle cabin due to a prescribed motion and task. Two additional examples are shared within this study; first, it was found that the model can predict the difference found between sitting forwards and backwards in an autonomous vehicle. Second, analysis of a respected and independent study into auxiliary display height shows that the model can predict both relative and absolute levels between the two display heights congruent to the original physical experiment. Conclusion: It has been shown that the tool has been successful in predicting motion sickness in autonomous vehicles and is therefore of great use in guiding new future mobility solutions in the ability to tune vehicle dynamics and control alongside vision and design attributes.
Approximate closed-form solutions of realistic true proportional navigation guidance using the Adomian decomposition method (2009)

Approximate closed-form solutions of the non-linear relative equations of motion of an interceptor pursuing a target under the realistic true proportional navigation (RTPN) guidance law are derived using the Adomian decomposition method in this article. In the literature, no study has been reported on derivation of explicit time-series solutions in closed form of the non-linear dynamic engagement equations under the RTPN guidance. The Adomian method provides an analytical approximation, requiring no linearization or direct integration of the non-linear terms. The complete derivation of the Adomian polynomials for the analysis of the dynamics of engagement under RTPN guidance is presented for deterministic ideal case, and non-ideal dynamics in the loop that comprises autopilot and actuator dynamics and target manoeuvre, as well as, for a stochastic case. Numerical results illustrate the applicability of the method.
A testbed for the evaluation of an interactive multimedia distance learning service (2002)

An overview of an experimental environment capable to support distance learning sessions is presented. In particular, the system described consists of specially equipped classrooms located in three Italian towns and linked by digital communication facilities, through which lectures are transmitted in real time in an interactive multimedia framework. Results of a three-year period of experiments with real university lectures are presented, along with the directions for further research and possibilities of improvement.
Enzalutamide for Hormone-Sensitive Metastatic Prostate Cancer (2019)

Level-1 evidence indicates that adding docetaxel, abiraterone, or apalutamide to standard androgen-deprivation therapy (ADT) can improve overall
Return of Research Results: General Principles and International Perspectives (2011)

Five years ago, an article co-written by two of us (Joly and Simard) presented an emerging trend to disclose certain individual genetic results to research participants. Since then, both technologies and research practices have evolved significantly. Given this rapid evolution, our goal is to provide updated and thorough guidance on this issue. Our paper begins by identifying the ethical principles that support the return of results: justice, beneficence, and respect for persons. Then, it presents the results of an analysis of international norms on the return of results, covering both general and individual research results. It reveals existing divergence and consensus on these topics within the international community. With the goal of promoting greater harmonization, we conclude by proposing a flexible framework for the return of individual research results.
An epidemiologic assessment of thrombotic risk factors for cardiovascular disease (1992)

A series of epidemiologic studies evaluating thrombotic risk factors for cardiovascular disease have recently been completed. These studies, which have focused primarily on abnormalities of blood rheology, platelet function and endogenous fibrinolysis, may prove useful in identifying patients at high risk for future vascular disease.