gebhart/patrepeval huggingface dataset:
Coarctation of the aorta in complex congenital heart disease: simultaneous repair via sternotomy (1990)

Coarctation of the aorta (CoA) is often associated with complex congenital heart disease. Patients with such a combination may not benefit from coarctectomy alone. Eight children who presented with complex malformations of the heart underwent simultaneous repair of CoA and intracardiac surgery via sternotomy. After extensive mobilization of the aortic arch, cardiopulmonary bypass was established. During the cooling phase for deep hypothermic circulatory arrest (six cases), a persistent temperature gradient between the upper and lower half of the body confirmed the significance of CoA. One child was operated upon in deep hypothermia with low flow and one underwent valve repair on cardiopulmonary bypass. Mobilization of the descending aorta enabled CoA resection and end-to-end anastomosis with a running absorbable suture. The average descending aortic cross-clamping time was 15 min. By this time, the patient had been cooled sufficiently for the intracardiac procedure. There were two operative deaths not related to coarctectomy. The remaining children showed no arm-to-leg pressure gradient. Five were discharged from hospital and one patient died late from septicaemia. In our hands, this technique has served to accomplish simultaneous relief of CoA and repair of the intracardiac lesion thus sparing critically ill infants the hazards of repeated procedures.
Inverse display characterization: A two‐step parametric model for digital displays (2008)

Abstract— A simple additivity model is often used as a basic model for digital‐display characterization. However, such a simple model cannot satisfy the needs of demanding color‐management applications all the time. On the other hand, systematic sampling of the color space and 3‐D interpolation is an expensive method in terms of measurement and computation time when precision is needed. This paper presents an enhanced method to characterize the XYZ ‐to‐ RGB transform of a digital display. This parametric method exploits the independence between the luminance variation of the electro‐optic response and the colorimetric responses for certain display types. The model is generally applicable to digital displays, including 3‐DMD projectors, single DMDs, CRTs, LCDs, etc. , if the independence condition is satisfied. While the problem to solve is a 3‐D‐to‐3‐D transformation (from XYZ to RGB ), the proposed parametric model is the composition of a 2‐D transform followed by a 1‐D transform. The 2‐D transform manages the chromatic aspects and, in succession, the 1‐D transform manages the luminance variations. This parametric digital model is applicable in the field of color management, with the objective of characterizing digital displays and applying a reference look such as a film look.
Heritable genotype contrast mining reveals novel gene associations specific to autism subgroups (2017)

Though the genetic etiology of autism is complex, our understanding can be improved by identifying genes and gene-gene interactions that contribute to the development of specific autism subtypes. Identifying such gene groupings will allow individuals to be diagnosed and treated according to their precise characteristics. To this end, we developed a method to associate gene combinations with groups with shared autism traits, targeting genetic elements that distinguish patient populations with opposing phenotypes. Our computational method prioritizes genetic variants for genome-wide association, then utilizes Frequent Pattern Mining to highlight potential interactions between variants. We introduce a novel genotype assessment metric, the Unique Inherited Combination support, which accounts for inheritance patterns observed in the nuclear family while estimating the impact of genetic variation on phenotype manifestation at the individual level. High-contrast variant combinations are tested for significant subgroup associations. We apply this method by contrasting autism subgroups defined by severe or mild manifestations of a phenotype. Significant associations connected 286 genes to the subgroups, including 193 novel autism candidates. 71 pairs of genes have joint associations with subgroups, presenting opportunities to investigate interacting functions. This study analyzed 12 autism subgroups, but our informatics method can explore other meaningful divisions of autism patients, and can further be applied to reveal precise genetic associations within other phenotypically heterogeneous disorders, such as Alzheimer's disease.
Radiation Tolerance (2016)

Abstract Life on earth was not exposed to high‐dose ultraviolet (UV) light or ionising radiation (IR) until the last century. Despite this fact, it is possible to isolate species from within the Bacteria and Archaea that display an unusually high resistance to the lethal effects of UV light and/or IR when compared to the rest of the tree of life. Questions concerning what mechanisms mediate this radiation tolerance and why radiotolerance evolved in an environment void of sources of high‐energy radiation define the study of these species. A great deal is known concerning the specific biochemical and physiological processes that counteract the damage caused by electromagnetic radiations, but almost all species express the proteins that mediate these processes. The nature of what distinguishes a radioresistant species from a radiosensitive species remains elusive. Key Concepts A small subset of Bacteria and Archaea express unusually high resistance to the lethal effects of UV and ionising radiations. Beyond experimental evaluation, there are no overt characteristics that predict radiation tolerance; species can be defined as radiation‐tolerant only empirically. UV and ionising radiations kill by altering the DNA structure in a manner that interferes with the irradiated cell's ability to propagate. A number of active and passive mechanisms are known to contribute to a species' radiation tolerance, but a comprehensive explanation for radioresistance in any single species has remained elusive. Endospores tolerate UV and ionising radiations by mechanisms not available to their vegetative forms. The flux of UV and ionising radiations on earth have never been great enough to explain why high‐level resistance to these stresses evolved; a number of hypotheses have been put forward to account for the existence of radioresistant phenotypes.
Sensoric Micro and Nano Systems (2019)

Art. 1900733, 3 S.
Assays for Alloreactive Responses by PCR (2007)

In organ transplantation, major efforts are currently developed to minimize or even to withdraw immunosuppressive drugs. Different protocols have therefore been proposed to induce graft tolerance, that is, the survival of an allograft in the absence of continuing immunosuppression. They generally involve pre-transplant conditioning followed by hematopoietic stem cell infusion. Follow-up of immune status is mandatory in this kind of protocol, in order to investigate tolerance and consequently to reduce or withdraw immunosuppression without graft rejection. However, assessment of the alloreactive response using currently available techniques is labor-intensive and requires significant volume of patient's blood. The implementation of such tolerance protocols is thus difficult in routine practice. In this chapter, we describe a novel real-time polymerase chain reaction method based on interferon-gamma and interleukin-2 mRNAs quantification that requires only 10 ml of blood. Moreover, results can be obtained within 48 h. A modified mixed lymphocyte reaction (MLR) using whole blood T lymphocytes as responsive cells and CD3-depleted peripheral blood mononuclear cells (PBMCs) as stimulators is described. An alternative, that is, the use of PBMC as responding cells instead of whole blood, is also depicted. We successfully applied the technique in the monitoring of anti-donor reactivity in living donor liver graft recipients. We suggest that this rapid MLR assay could be valuable for the monitoring of patients undergoing solid organ or hematopoietic stem cell transplantation.
Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging data (2018)

Calcium imaging has revolutionized systems neuroscience, providing the ability to image large neural populations with single-cell resolution. The resulting datasets are quite large, which has presented a barrier to routine open sharing of this data, slowing progress in reproducible research. State of the art methods for analyzing this data are based on non-negative matrix factorization (NMF); these approaches solve a non-convex optimization problem, and are effective when good initializations are available, but can break down in low-SNR settings where common initialization approaches fail. Here we introduce an approach to compressing and denoising functional imaging data. The method is based on a spatially-localized penalized matrix decomposition (PMD) of the data to separate (low-dimensional) signal from (temporally-uncorrelated) noise. This approach can be applied in parallel on local spatial patches and is therefore highly scalable, does not impose non-negativity constraints or require stringent identifiability assumptions (leading to significantly more robust results compared to NMF), and estimates all parameters directly from the data, so no hand-tuning is required. We have applied the method to a wide range of functional imaging data (including one-photon, two-photon, three-photon, widefield, somatic, axonal, dendritic, calcium, and voltage imaging datasets): in all cases, we observe ~2-4x increases in SNR and compression rates of 20-300x with minimal visible loss of signal, with no adjustment of hyperparameters; this in turn facilitates the process of demixing the observed activity into contributions from individual neurons. We focus on two challenging applications: dendritic calcium imaging data and voltage imaging data in the context of optogenetic stimulation. In both cases, we show that our new approach leads to faster and much more robust extraction of activity from the data.
A Standardized Letter of Recommendation for Residency Application (1999)

Emergency medicine (EM) program directors have expressed a desire for more evaluative data to be included in application materials. This is consistent with frustrations expressed by program directors of multiple specialties, but mostly by those in specialties with more competitive matches. Some of the concerns about traditional narrative letters of recommendation included lack of uniform information, lack of relative value given for interval grading, and a perception of ambiguity with regard to terminology. The Council of Emergency Medicine Residency Directors established a task force in 1995 that created a standardized letter of recommendation form. This form, to be completed by EM faculty, requests that objective, comparative, and narrative information be reported regarding the residency applicant.
Parallel Algorithms for Constructing Data Structures for Fast Multipole Methods (2013)

We present efficient algorithms to build data structures and the lists needed for fast multipole methods. The algorithms are capable of being efficiently implemented on both serial, data parallel GPU and on distributed architectures. With these algorithms it is possible to map the FMM efficiently on to the GPU or distributed heterogeneous CPU-GPU systems. Further, in dynamic problems, as the distribution of the particles change, the reduced cost of building the data structures improves performance. Using these algorithms, we demonstrate example high fidelity simulations with large problem sizes by using FMM on both single and multiple heterogeneous computing facilities equipped with multi-core CPU and many-core GPUs.
Nanoscale Engineering of Closely-Spaced Electronic Spins in Diamond (2016)

Numerous theoretical protocols have been developed for quantum information processing with dipole-coupled solid-state spins. Nitrogen vacancy (NV) centers in diamond have many of the desired properties, but a central challenge has been the positioning of NV centers at the nanometer scale that would allow for efficient and consistent dipolar couplings. Here we demonstrate a method for chip-scale fabrication of arrays of single NV centers with record spatial localization of about 10 nm in all three dimensions and controllable inter-NV spacing as small as 40 nm, which approaches the length scale of strong dipolar coupling. Our approach uses masked implantation of nitrogen through nanoapertures in a thin gold film, patterned via electron-beam lithography and dry etching. We verified the position and spin properties of the resulting NVs through wide-field super-resolution optically detected magnetic resonance imaging.
Characterization of the PEO−PPO−PEO Triblock Copolymer and Its Application as a Separation Medium in Capillary Electrophoresis (1997)

The Pluronic polyol F127, PEO99PPO69PEO99 (PEO and PPO being poly(ethylene oxide) and poly(propylene oxide), respectively) has the potential to be used as an effective separation medium in capillary electrophoresis (CE) for the separation of biomacromolecules such as DNA fragments and proteins. Static light scattering (SLS), dynamic light scattering (DLS), small-angle neutron scattering (SANS), and small-angle X-ray scattering (SAXS) were used to characterize the solution properties and the microstructures of F127 in the same electrophoresis buffer used in CE. In the dilute solution region, F127 in CE buffer forms micelles similar to that in water. At high solution concentrations, micelles tend to pack into some crystalline forms with relatively well-structured PPO centers. By using a combination of SANS and SAXS results, we are able to conclusively determine the gellike structure to have a face-centered cubic lattice. The effects of solvent, polymer concentration, temperature, and sample preparation procedure on the gel structure were studied. In the gellike region the aggregation number and also the micellar size are not sensitive to both the concentration change and the temperature change. The results of DNA electrophoretic migration in F127 gels also support these findings.
<i>N</i>,<i>N</i>′-Bis[(<i>E</i>)-4-nitrobenzylidene]-4,4′-oxydianiline (2009)

The title compound, C(26)H(18)N(4)O(5), can be regarded as an extended ether with two terminal nitro groups. The two aryl rings bonded to the central O atom form a dihedral angle of 75.72 (6)°, and the terminal nitro groups are slightly twisted [by 6.4 (2) and 3.3 (3)°] from the benzene rings to which they are attached. The crystal packing exhibits weak inter-molecular C-H⋯O hydrogen bonds and π-π inter-actions [centroid-centroid distances = 3.794 (3) Å].
The cellular expression and proteolytic processing of the amyloid precursor protein is independent of TDP-43 (2020)

Alzheimer's disease (AD) is a neurodegenerative condition, of which one of the cardinal pathological hallmarks is the extracellular accumulation of amyloid β (Aβ) peptides. These peptides are generated via proteolysis of the amyloid precursor protein (APP), in a manner dependent on the β-secretase, BACE1 and the multicomponent γ-secretase complex. Recent data also suggest a contributory role in AD of transactive response DNA binding protein 43 (TDP-43). There is little insight into a possible mechanism linking TDP-43 and APP processing. To this end, we used cultured human neuronal cells to investigate the ability of TDP-43 to interact with APP and modulate its proteolytic processing. Immunocytochemistry showed TDP-43 to be spatially segregated from both the extranuclear APP holoprotein and its nuclear C-terminal fragment. The latter (APP intracellular domain) was shown to predominantly localise to nucleoli, from which TDP-43 was excluded. Furthermore, neither overexpression of each of the APP isoforms nor siRNA-mediated knockdown of APP had any effect on TDP-43 expression. Doxycycline-stimulated overexpression of TDP-43 was explored in an inducible cell line. Overexpression of TDP-43 had no effect on expression of the APP holoprotein, nor any of the key proteins involved in its proteolysis. Furthermore, increased TDP-43 expression had no effect on BACE1 enzymatic activity or immunoreactivity of Aβ1-40, Aβ1-42 or the Aβ1-40:Aβ1-42 ratio. Also, siRNA-mediated knockdown of TDP-43 had no effect on BACE1 immunoreactivity. Taken together, these data indicate that TDP-43 function and/or dysfunction in AD is likely independent from dysregulation of APP expression and proteolytic processing and Aβ generation.
An Intrinsically Glassy Metallic Coordination Polymer Showing Thermally and Aerobically Robust Conductivity (2022)

Abstract Conducting organic materials, such as doped organic polymers, (1) molecular conductors, (2,3) and emerging coordination polymers, (4) underpin technologies ranging from displays to flexible electronics. (5) Realizing high electrical conductivity in traditionally insulating organic materials necessitates tuning their electronic structure through chemical doping. (6) Furthermore, even materials that are intrinsically conductive, such as single-component molecular conductors, (7,8) require crystallinity for metallic behavior. However, commercial conducting polymers are often purposefully amorphous to aid in durability and processability. (9,10) Using molecular design to engender high conductivity in undoped amorphous materials would enable tunable and robust conductivity in many applications, but there are no intrinsically conducting organic materials which maintain high conductivity when disordered. Here we show that the completely amorphous coordination polymer Ni tetrathiafulvalene tetrathiolate (NiTTFtt) displays intrinsic metallic conductivity. Despite its disordered structure, NiTTFtt exhibits remarkably high electronic conductivity (1280 S/cm) and intrinsically glassy metallic behavior. Analysis with advanced theory shows that these properties are enabled by strong molecular overlap and correlation that are robust to structural perturbations. This unusual set of structural and electronic features results in remarkably stable organic conductivity which is maintained in air for weeks and at temperatures up to 140 °C. Our results demonstrate that molecular design can enable metallic conductivity even in heavily disordered materials. This both raises fundamental questions about how band-like transport can exist in the absence of periodic structure as well as suggests exciting new applications for these materials.
Cytotoxic Compounds of <i>Schizolaena hystrix</i> from the Madagascar Rainforest (2006)

Bioassay-guided fractionation of a crude ethanol extract from a Madagascar collection of Schizolaena hystrix afforded the two new long-chain compounds, 3 S-acetoxyeicosanoic acid ethyl ester ( 1) and 3 S-acetoxydoeicosanoic acid ( 2), and the known long-chain compound 3 S-acetoxyeicosanoic acid ( 3). In addition, the long-chain alcohol 1-hydroxydodecan-2-one ( 7), as well as the new flavonoid schizolaenone C ( 4) and the two known flavonoids diplacol ( 5) and 3'-prenylnaringenin ( 6) were isolated from a methanol extract of the same plant. Isolation and structure elucidation of the novel compounds and the cytotoxicities of all the isolates are reported.
Auxotrophic Mutations Reduce Tolerance of Saccharomyces cerevisiae to Very High Levels of Ethanol Stress (2015)

Very high ethanol tolerance is a distinctive trait of the yeast Saccharomyces cerevisiae with notable ecological and industrial importance. Although many genes have been shown to be required for moderate ethanol tolerance (i.e., 6 to 12%) in laboratory strains, little is known of the much higher ethanol tolerance (i.e., 16 to 20%) in natural and industrial strains. We have analyzed the genetic basis of very high ethanol tolerance in a Brazilian bioethanol production strain by genetic mapping with laboratory strains containing artificially inserted oligonucleotide markers. The first locus contained the ura3Δ0 mutation of the laboratory strain as the causative mutation. Analysis of other auxotrophies also revealed significant linkage for LYS2, LEU2, HIS3, and MET15. Tolerance to only very high ethanol concentrations was reduced by auxotrophies, while the effect was reversed at lower concentrations. Evaluation of other stress conditions showed that the link with auxotrophy is dependent on the type of stress and the type of auxotrophy. When the concentration of the auxotrophic nutrient is close to that limiting growth, more stress factors can inhibit growth of an auxotrophic strain. We show that very high ethanol concentrations inhibit the uptake of leucine more than that of uracil, but the 500-fold-lower uracil uptake activity may explain the strong linkage between uracil auxotrophy and ethanol sensitivity compared to leucine auxotrophy. Since very high concentrations of ethanol inhibit the uptake of auxotrophic nutrients, the active uptake of scarce nutrients may be a major limiting factor for growth under conditions of ethanol stress.
Simple Heuristics Yield Provable Algorithms for Masked Low-Rank Approximation (2019)

In $masked\ low-rank\ approximation$, one is given $A \in \mathbb{R}^{n \times n}$ and binary mask matrix $W \in \{0,1\}^{n \times n}$. The goal is to find a rank-$k$ matrix $L$ for which: $$cost(L) = \sum_{i=1}^{n} \sum_{j = 1}^{n} W_{i,j} \cdot (A_{i,j} - L_{i,j} )^2 \leq OPT + ε\|A\|_F^2 ,$$ where $OPT = \min_{rank-k\ \hat{L}} cost(\hat L)$ and $ε$ is a given error parameter. Depending on the choice of $W$, this problem captures factor analysis, low-rank plus diagonal decomposition, robust PCA, low-rank matrix completion, low-rank plus block matrix approximation, and many problems. Many of these problems are NP-hard, and while some algorithms with provable guarantees are known, they either 1) run in time $n^{Ω(k^2/ε)}$ or 2) make strong assumptions, e.g., that $A$ is incoherent or that $W$ is random. In this work, we show that a common polynomial time heuristic, which simply sets $A$ to $0$ where $W$ is $0$, and then finds a standard low-rank approximation, yields bicriteria approximation guarantees for this problem. In particular, for rank $k' &gt; k$ depending on the $public\ coin\ partition\ number$ of $W$, the heuristic outputs rank-$k'$ $L$ with cost$(L) \leq OPT + ε\|A\|_F^2$. This partition number is in turn bounded by the $randomized\ communication\ complexity$ of $W$, when interpreted as a two-player communication matrix. For many important examples of masked low-rank approximation, including all those listed above, this result yields bicriteria approximation guarantees with $k' = k \cdot poly(\log n/ε)$. Further, we show that different models of communication yield algorithms for natural variants of masked low-rank approximation. For example, multi-player number-in-hand communication complexity connects to masked tensor decomposition and non-deterministic communication complexity to masked Boolean low-rank factorization.
Search-based Evaluation from Truth Transcripts for Voice Search Applications (2016)

Voice search applications are typically evaluated by comparing the predicted query to a reference human transcript, regardless of the search results returned by the query. While we find that an exact transcript match is highly indicative of user satisfaction, a transcript which does not match the reference still produces satisfactory search results a significant fraction of the time. This paper therefore proposes an evaluation method that compares the search results of the speech recognition hypotheses with the search results produced by a human transcript. Compared with a strict sentence match, a human evaluation shows that search result overlap is a better predictor of (a) user satisfaction and (b) search result click-through. Finally, we propose a model predicting the Expected Search Satisfaction Rate (ESSR), conditioned on search overlap outcomes. On a held out set of 1036 voice search queries, our model predicted an ESSR within 0.9% (relative) of the ground truth satisfaction averaged over 3 human judges.