gebhart/patrepeval huggingface dataset:
Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019 (2021)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kinetics remain understudied, including the impact of remdesivir. In hospitalized individuals, peak sputum viral load occurred in week 2 of symptoms, whereas viremia peaked within 1 week of symptom-onset, suggesting early systemic seeding of SARS-CoV-2. Remdesivir treatment was associated with faster viral decay.
Intrarenal handling of proteins in rats using fractional micropuncture technique (1992)

Previous micropuncture studies on protein handling along the nephron could not exclude the possibility of contamination by extratubular proteins. Thus we developed a fractional micropuncture method. Renal tubules were punctured with an outer puncture pipette, into which an inner collection pipette was inserted repeatedly to collect tubular fluid, usually up to four fractions. The albumin concentration of tubular fluid was highest in the first fraction and gradually decreased to a constant level, indicating physiological albumin concentrations. On the other hand, low-molecular-weight protein (LMWP) concentrations showed no significant difference among the four fractions. By plotting the protein delivery in the fourth fraction along the nephron, glomerular filtrated protein concentrations were estimated by extrapolating the tubular fluid-to-plasma inulin concentration ratio into one. The glomerular filtrated albumin was 22.9 micrograms/ml (0.00062 in filtration coefficient), and that of LMWP was 72.1 (0.988). Albumin was almost evenly reabsorbed in early (37%) and late (34%) proximal convoluted tubules and the straight tubules (23%). On the other hand, LMWP was more strongly reabsorbed in the early proximal convoluted tubules (54%) than in the late ones (28%) or the straight portion (5%). The fractional micropuncture procedure provides direct evidence of protein handling along the nephron without extratubular protein contamination.
Electron and hole mobility enhancements in sub-10 nm-thick strained silicon directly on insulator fabricated by a bond and etch-back technique (2004)

Electron and hole mobility enhancements are studied in Ge-free strained silicon directly on insulator fabricated by a bond and etch-back technique, for the first time. For inversion charge densities of 10/sup 13/ cm/sup -2/, electron and hole mobility enhancements of 100% (n-MOSFET, 30% effective Ge content, 15 nm-thick) and 50% (p-MOSFET, 40% effective Ge, 6 nm-thick), respectively are measured in fully depleted strained Si. For a biaxial strain level of 1.25% (30% effective Ge), hole mobility is the same for body thicknesses of 25 and 13 nm, and drops by no more than 5% for a body thickness of 8.5 nm. There is no evidence of strain relaxation, despite a generous thermal budget.
Rapid T cell–based identification of human tumor tissue antigens by automated two-dimensional protein fractionation (2010)

Identifying the antigens that have the potential to trigger endogenous antitumor responses in an individual cancer patient is likely to enhance the efficacy of cancer immunotherapy, but current methodologies do not efficiently identify such antigens. This study describes what we believe to be a new method of comprehensively identifying candidate tissue antigens that spontaneously cause T cell responses in disease situations. We used the newly developed automated, two-dimensional chromatography system PF2D to fractionate the proteome of human tumor tissues and tested protein fractions for recognition by preexisting tumor-specific CD4+ Th cells and CTLs. Applying this method using mice transgenic for a TCR that recognizes an OVA peptide presented by MHC class I, we demonstrated efficient separation, processing, and cross-presentation to CD8+ T cells by DCs of OVA expressed by the OVA-transfected mouse lymphoma RMA-OVA. Applying this method to human tumor tissues, we identified MUC1 and EGFR as tumor-associated antigens selectively recognized by T cells in patients with head and neck cancer. Finally, in an exemplary patient with a malignant brain tumor, we detected CD4+ and CD8+ T cell responses against two novel antigens, transthyretin and calgranulin B/S100A9, which were expressed in tumor and endothelial cells. The immunogenicity of these antigens was confirmed in 4 of 10 other brain tumor patients. This fast and inexpensive method therefore appears suitable for identifying candidate T cell antigens in various disease situations, such as autoimmune and malignant diseases, without being restricted to expression by a certain cell type or HLA allele.
Propagation and diffraction of locally excited surface plasmons (2001)

With the use of optical near-field techniques, it is now possible to excite or observe surface plasmons with high lateral resolution. A theoretical study is presented of surface plasmon excitation by near-field optical probes and the influence of well-defined structures on surface plasmon propagation and surface plasmon detection in the far field. The generation and the diffraction of the surface plasmon is calculated by using a theoretical scheme founded upon a first-order perturbation expansion of the Rayleigh-Fano method. A very good agreement is obtained between numerical and experimental results. The theoretical tools used should prove a useful guideline for future experiments of nanooptics with surface plasmons.
Reverse Micelle Based Growth of Zincophosphate Sodalite:  Examination of Crystal Growth (1996)

Formation of zincophosphates from zinc and phosphate containing reverse micelles (water droplets in hexane) has been examined. The frameworks formed resemble those made by conventional hydrothermal synthesis. Dynamics of crystal growth are however quite different and form the main focus of this study. In particular, the formation of zincophosphate with the sodalite framework was examined in detail. The intramicellar pH was found to have a strong influence on crystal growth. Crystals with a cubic morphology were formed directly from the micelles, without an apparent intermediate amorphous phase over a period of 4 days by a layer-by-layer growth at the intramicellar pH of 7.6. At a pH of 6.8, an amorphous precipitate rapidly sediments in hours. Sodalite was eventually formed from this settled phase via surface diffusion and reconstruction within 4 days. With a rotating cell, it was possible to minimize sedimentation and crystals were found to grow epitaxially from the spherical, amorphous particles. Intermediate pH's of 7.2 led to formation of aggregated sodalite crystals prior to settling, again without any indication of an intermediate amorphous phase. These diverse pathways were possible due to changes in intramicellar supersaturation conditions by minor changes in pH. In contrast, conventional syntheses in this pH range all proceeded by similar crystallization pathways through an amorphous gel. This study establishes that synthesis of microporous frameworks is not only possible in reverse micellar systems, but they also allow examination of possible crystallization pathways.
On-Top Plasty at the Level of the Metatarsal Neck for Treatment of Polydactyly (2022)

Polydactyly is a common deformity of the limbs, and excision of the extra digit has shown good results in the vast majority of patients. However, this treatment approach may not suitable for all cases of polydactyly. Some complex surgical procedures are required to treat rare forms of polydactyly and achieve satisfactory correction. Here, we report the use of on-top plasty technique for treating polydactyly between the 4th and 5th metatarsals with concomitant angulation of the 5th metatarsophalangeal joint. We performed the first osteotomy at the neck of metatarsal bone by "grafting" the distal polydactyly with the normal axis to the 5th metatarsal bone. Excision of the extra toe was accompanied by simultaneous restoration of the 5th toe axis and decrease in the width of the forefoot. Finally, both appearance and function could be improved. With this novel method, the complete osteoarticular structure and weight-bearing structure of foot were well-reconstructed. Based on the findings, we recommend that for the surgery of polydactyly, the beneficial parts should be preserved for reconstruction, and the tailored and personalized approach could be adopted.
Identification and transcription control of fission yeast genes repressed by an ammonium starvation growth arrest (2000)

In fission yeast Schizosaccharomyces pombe, ammonium starvation induces a growth arrest, a cell cycle exit in G(1) and a further switch to meiosis. This process is regulated by the cAMP-dependent protein kinase and the Wis1-dependent MAP kinase cascade, and downstream transcription factors. In order to understand how cells adapt their genetic programme to the switch from mitotic cycling to starvation, a differential transcript analysis comparing mRNA from exponentially growing and ammonium-starved cells was performed. Genes repressed by this stimulus mainly concern cell growth, i.e. protein synthesis and global metabolism. Comparison of the expression of two of them, the ribosomal proteins Rps6 and TCTP, in many different growing conditions, evidenced a strong correlation, suggesting that their transcriptions are coordinately regulated. Nevertheless, by repeating the ammonium starvation on strains constitutively activated for the PKA pathway (Deltacgs1), or unable to activate the Wis1-dependent MAP kinase pathway (Deltawis1), or with both characteristics (Deltacgs1+Deltawis1), the transcriptional inhibition was found to be governed either by the PKA pathway, or by the Wis1 pathway, or by both. These results suggest that during the switch from exponential growth to ammonium starvation, cell homeostasis is maintained by downregulating the transcription of the most expressed genes by a PKA and a Wis1-dependent process. Accession Nos for the S30 and L14 ribosomal protein cDNA sequences are AJ2731 and AJ2732, respectively.
A simplified angular multigrid method to accelerate S{sub N} calculations (1999)

In problems with optically thick regions and high scattering ratios (c {minus} ratio = {sigma}{sub s}/{sigma}{sub t}), particles that are making a large number of scattering collisions in a single energy group contribute significantly to scalar flux distribution; consequently, the convergence of the source iteration (SI) method can become very slow. For certain cross-section libraries, groups in the thermal energy range may be very broad, and particles may undergo many scattering events before being removed from the group. One remedy to fix the slow convergence is to narrow the energy group ranges; however, this means that the transport equation must be solved for more groups, which may lead to further computational inefficiency. Hence, numerous techniques have been devised to accelerate the SI method, such as rebalance, diffusion synthetic acceleration (DSA), and multigrid acceleration schemes. Multigrid acceleration is a general type of acceleration method, which has been applied to transport calculations by using it directly for the S{sub N} equations and/or for the DSA equations. The basic principle of the multigrid method is to use a sequence of coarse and fine grids to obtain an accelerated solution on the fine grid. Here, the authors briefly explain the general idea of themore » multigrid method.« less
Opportunistic Multi-Layer Transmission over Unknown Channels (2021)

We use the received bit information rate (RBIR) to analyze the performance of multi-layer transmission when combined with hybrid automatic repeat request (HARQ). The different layers are obtained from ordinary Gray-coded M-QAM and used for transmitting log <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> (M) codewords in parallel, exploiting that the different bits in Gray-coded M-QAM have very different reliability. The performance is analyzed when different layers are decoded in parallel (independently) as well as when successive decoding is used. In addition, we study how the RBIR can be used to select a suitable layer for a retransmission to further improve the performance. Simulation results based on a Wi-Fi like physical layer show that a significant gain compared to the standard approach can be achieved by using basic multilayer transmission, and also that using successive decoding and carefully selecting what layer to use for retransmission can give further gains.
A Study of Augmented Reality based Visualization using Shape Information of Building Information Modeling (2012)

기존의 건축계획 및 설계과정에서는 건축물 내 외부의 공간감을 확인하기 위해 건물모형을 제작하였으나 건물모형은 비교적 많은 제작 시간과 노력이 들며 건물의 내부 정보를 파악하기에 어려움이 따른다. 이를 보완하기 위해 기존 설계, 계획 과정과 그에 대한 가시화 방법으로써 CAD툴을 사용하여 건물 모형으로는 파악하기 어려운 건물 내부 정보를 가시화 할 수 있었지만, 건물모형에서 확인할 수 있는 부피감을 확인하기에는 부족함이 존재한다. 기본적으로 CAD는 설계에 목적을 두고 만들어진 프로그램이며 일반적인 가시화 환경인 2차원 모니터 화면상에서 3차원 건물을 보여주게 되므로 공간에 대한 인지적 몰입감을 만족시키기에는 부족하다. 본 논문에서는 BIM 형상정보 데이터를 일련의 소프트웨어로 가공하여 증강현실 컨텐츠로 변환하는 과정을 소개한다. 이는 건축계획 및 설계과정에서 형상정보가 수정될 경우 최종 가시화까지 소요되는 비용과 시간을 단축시킬 수 있다. 또한 BIM 형상정보를 증강현실기법을 이용하여 3차원 인지공간에서 가시화함으로써 3차원 건물의 내 외부 공간정보를 분석하기가 용이하다. 또한 건물의 내 외부 정보를 증강현실 환경에서 효과적으로 조작할 수 있도록 건축 요소의 제거, 슬라이스컷 등 다양한 인터랙션을 제안한다. In the current construction planning and designing process, an architectural miniature model was designed to verify the interior or exterior spatial sense of a building structure, but building of the miniature model is demand much more effort and time; in addition to this it has limitation to identify interior information of the building. For a complement of it, CAD would be used in the existing planning and designing process to visualize the building information, but its visualization is not satisfactory for the 3D volume which could be easily verified with the miniature model. CAD is the specific software for designing building structures and the 3D results are usually rendered on 2D monitor screen. Therefore, there is a shortage of cognitive immersion for the 3D space. In this paper, we introduce the conversion process of BIM shape data into the Augmented Reality contents by using a series of softwares. As a result of modification on construction plan or design we reduced the cost and time to reconstruct the final visualization. We have shown that the interior or exterior information of the building structures are easily visualized with BIM shape data on augmented reality environment. Several proposed interaction methods, such as rem oval of building components, and slice-cut operation, provide the user for the effective manipulation of models on the augmented reality environment.
Optimal Management of Topside Diluent Injection for a Heavy Oil Field (2017)

Abstract Heavy oil fields can be developed using diluent (light oil, condensate, etc.) injection at the well level as a flow improver. However, diluent can also be injected at the surface, as used in Canadian heavy oil production. Benefits of topside diluent injection include among others (1) improved oil/water separation in the surface processing facility, (2) improved viscosity, and (3) better final crude quality. Such blending activities are often associated with additional OPEX due to the high price of diluent, which can add significant costs to a development. This paper describes an Integrated Asset Modelling (IAM) solution designed to minimize the topside diluent requirement while honouring technical and market crude specifications. The case studied is an offshore heavy oil field consistings of two reservoirs with API gravities of 14 and 12, and oil viscosities at reservoir conditions of 70 cp and 500 cp. The production facilities include a two-stage surface processing facility followed by a coalescer aimed to separate the water from the crude. Diluent is injected in the surface processing facility prior to the second stage separator. Operating variables include (1) the topside diluent injection rate and (2) the temperature of the second stage separator. The difficulty of the production optimization problem lies in the non-linearity of the process and viscosity models, and the consistency of the fluid’s PVT description throughout the production system. The proposed optimization solution is coupled with a reservoir simulator to determine optimal topside diluent requirements over time and foresee eventual bottlenecks in the surface infrastructure design. The proposed solution can also be used as a real-time management tool during the production phase to find the optimal operating point based on real-time data. The optimal operating point ensures the lowest diluent consumption while meeting all system constraints, providing the framework for significant cost savings.
Intermittent administration of bovine PTH-(1–34) increases serum 1,25-dihydroxyvitamin D concentrations and spinal bone density in senile (23 month) rats (1992)

We examined the effect of intermittent administration of bovine parathyroid hormone (1-34) (bPTH) on spinal bone mineral content (BMC) and bone mineral density (BMD), serum 1,25-dihydroxyvitamin D concentrations, and serum markers of osteoblast function in senile male and female rats (23 and 24 months of age, respectively). Sexually mature young (3 month) male rats were similarly treated for comparison. bPTH administration increased serum osteocalcin concentrations without changing serum inorganic phosphate or calcium concentrations in either group of old animals. In young animals, PTH administration increased the serum calcium and inorganic phosphate concentrations significantly (p less than 0.05), although values remained within the normal range. In the vehicle-treated male rats, serum 1,25-dihydroxyvitamin D concentrations were lower in the senile than in the young animals (18 +/- 5 versus 47 +/- 6 pg/ml, p less than 0.05). PTH administration resulted in significantly increased serum 1,25-dihydroxyvitamin D concentrations in the senile and young male animals (both, p less than 0.05) and the final mean serum 1,25-dihydroxyvitamin D concentrations were not statistically different (68 +/- 9 versus 85 +/- 6 pg/ml respectively; p = NS). Serum 1,25-dihydroxyvitamin D concentrations were significantly (p less than 0.05) higher in the PTH-treated senile female rats than the sex-matched, vehicle-treated controls. The pretreatment spinal BMC and BMD as assessed by dual-energy x-ray absorptiometry (DEXA) were significantly higher in the senile male animals than in the young animals. Spinal BMC and BMD decreased in the vehicle-treated senile male rats (p less than 0.05) over the 3 weeks of the study despite a gain in weight.(ABSTRACT TRUNCATED AT 250 WORDS)
Modelling and Optimization for Multi-hop Wireless Networks Using Fixed Point and Automatic Differentiation (2008)

We develop and evaluate a new method for estimating and optimizing various performance metrics of multi-hop wireless networks, including MANETs. We introduce a simple approximate (throughput) loss model that couples the physical, MAC and routing layers effects. The model provides quantitative statis
Optical 64QAM Transmitter using Tandem IQ Modulators with Balanced Complexity in Electronics and Optics (2013)

Instead of using eight-level electronics or highly-integrated optics, 64QAM generation is experimentally demonstrated using two tandem IQ modulators with four-level electronics. The complexity in electronics and optics is well-balanced. 16QAM and 36QAM are also synthesized.
Fixed Points of Generalized Approximate Message Passing with Arbitrary\n Matrices (2013)

The estimation of a random vector with independent components passed through\na linear transform followed by a componentwise (possibly nonlinear) output map\narises in a range of applications. Approximate message passing (AMP) methods,\nbased on Gaussian approximations of loopy belief propagation, have recently\nattracted considerable attention for such problems. For large random\ntransforms, these methods exhibit fast convergence and admit precise analytic\ncharacterizations with testable conditions for optimality, even for certain\nnon-convex problem instances. However, the behavior of AMP under general\ntransforms is not fully understood. In this paper, we consider the generalized\nAMP (GAMP) algorithm and relate the method to more common optimization\ntechniques. This analysis enables a precise characterization of the GAMP\nalgorithm fixed-points that applies to arbitrary transforms. In particular, we\nshow that the fixed points of the so-called max-sum GAMP algorithm for MAP\nestimation are critical points of a constrained maximization of the posterior\ndensity. The fixed-points of the sum-product GAMP algorithm for estimation of\nthe posterior marginals can be interpreted as critical points of a certain free\nenergy.\n
A proof of concept for structure-based vaccine design targeting RSV in humans (2019)

Technologies that define the atomic-level structure of neutralization-sensitive epitopes on viral surface proteins are transforming vaccinology and guiding new vaccine development approaches. Previously, iterative rounds of protein engineering were performed to preserve the prefusion conformation of the respiratory syncytial virus (RSV) fusion (F) glycoprotein, resulting in a stabilized subunit vaccine candidate (DS-Cav1), which showed promising results in mice and macaques. Here, phase I human immunogenicity data reveal a more than 10-fold boost in neutralizing activity in serum from antibodies targeting prefusion-specific surfaces of RSV F. These findings represent a clinical proof of concept for structure-based vaccine design, suggest that development of a successful RSV vaccine will be feasible, and portend an era of precision vaccinology.
Quality Improvement Goals for Acute Kidney Injury (2019)

AKI is a global concern with a high incidence among patients across acute care settings. AKI is associated with significant clinical consequences and increased health care costs. Preventive measures, as well as rapid identification of AKI, have been shown to improve outcomes in small studies. Providing high-quality care for patients with AKI or those at risk of AKI occurs across a continuum that starts at the community level and continues in the emergency department, hospital setting, and after discharge from inpatient care. Improving the quality of care provided to these patients, plausibly mitigating the cost of care and improving short- and long-term outcomes, are goals that have not been universally achieved. Therefore, understanding how the management of AKI may be amenable to quality improvement programs is needed. Recognizing this gap in knowledge, the 22nd Acute Disease Quality Initiative meeting was convened to discuss the evidence, provide recommendations, and highlight future directions for AKI-related quality measures and care processes. Using a modified Delphi process, an international group of experts including physicians, a nurse practitioner, and pharmacists provided a framework for current and future quality improvement projects in the area of AKI. Where possible, best practices in the prevention, identification, and care of the patient with AKI were identified and highlighted. This article provides a summary of the key messages and recommendations of the group, with an aim to equip and encourage health care providers to establish quality care delivery for patients with AKI and to measure key quality indicators.