gebhart/patrepeval huggingface dataset:
Acute Myeloid Leukemia Affects Mouse Sperm Parameters, Spontaneous Acrosome Reaction, and Fertility Capacity (2019)

Leukemia is one of the most common cancers in patients of reproductive age. It is well known that chemotherapy, used as anti-cancer therapy, adversely affects male fertility. Moreover, the negative effect of leukemia on sperm quality, even before chemotherapy treatment, has been reported. However, the mechanisms behind this disease's effect on sperm quality remains unknown. In this study, we examine the direct effect of leukemia and chemotherapy alone and in combination on sperm parameters and male fertility. For this, we developed an acute myeloid leukemia (AML) mouse model (mice were treated with AML cells C1498 and developed leukemia); these mice then received cytarabine chemotherapy. Our findings reveal a significant reduction in sperm concentration and motility and a significant increase in abnormal morphology and spontaneous acrosome reaction of the sperm following AML and chemotherapy treatment, alone and in combination. We also found a reduction in male fertility and the number of delivered offspring. Our results support previous findings that AML impairs sperm parameters and show for the first time that AML increases spontaneous acrosome reaction and decreases male fertility capacity and number of offspring.
Biocatalytic Synthesis of Fluorescent Conjugated Polyserotonin (2019)

Polyserotonin was enzymatically synthesized using Horseradish peroxidase (HRP) as the catalyst. This novel conjugated polymer exhibited good fluorescent properties with significantly higher Stokes shift than its monomer. The enzymatic polymerization eliminated the need for extensive purification of the product (typically necessary for the removal of residual metal catalyst) allowing the product to be naturally fluorescent as synthesized. The reaction was monitored using UV-Vis spectrophotometry and the polymers were characterized using Fluorescence, Fourier Transform Infrared Spectroscopy (FTIR) and Thermogravimetry. The possibility of using polyserotonin for the detection of nitro-aromatic compounds, including 2,4-dinitrotoluene (DNT) and trinitrotoluene (TNT), through fluorescence quenching at parts per million levels in solution has also been demonstrated.
Sustainable Infrastructure Engineering: Integrating Material and Structural Design with Life Cycle Analysis (2006)

Peer Reviewed
A reconfigurable computing platform for plume tracking with mobile sensor networks (2006)

Much work has been undertaken recently toward the development of low-power, high-performance sensor networks. There are many static remote sensing applications for which this is appropriate. The focus of this development effort is applications that require higher performance computation, but still involve severe constraints on power and other resources. Toward that end, we are developing a reconfigurable computing platform for miniature robotic and human-deployed sensor systems composed of several mobile nodes. The system provides static and dynamic reconfigurability for both software and hardware by the combination of CPU (central processing unit) and FPGA (field-programmable gate array) allowing on-the-fly reprogrammability. Static reconfigurability of the hardware manifests itself in the form of a "morphing bus" architecture that permits the modular connection of various sensors with no bus interface logic. Dynamic hardware reconfigurability provides for the reallocation of hardware resources at run-time as the mobile, resource-constrained nodes encounter unknown environmental conditions that render various sensors ineffective. This computing platform will be described in the context of work on chemical/biological/radiological plume tracking using a distributed team of mobile sensors. The objective for a dispersed team of ground and/or aerial autonomous vehicles (or hand-carried sensors) is to acquire measurements of the concentration of the chemical agent from optimal locations and estimate its source and spread. This requires appropriate distribution, coordination and communication within the team members across a potentially unknown environment. The key problem is to determine the parameters of the distribution of the harmful agent so as to use these values for determining its source and predicting its spread. The accuracy and convergence rate of this estimation process depend not only on the number and accuracy of the sensor measurements but also on their spatial distribution over time (the sampling strategy). For the safety of a human-deployed distribution of sensors, optimized trajectories to minimize human exposure are also of importance. The systems described in this paper are currently being developed. Parts of the system are already in existence and some results from these are described.
Semiconductor-nanocrystal/conjugated polymer thin films (2023)

The invention described herein provides for thin films and methods of making comprising inorganic semiconductor-nanocrystals dispersed in semiconducting-polymers in high loading amounts. The invention also describes photovoltaic devices incorporating the thin films.
Gene Expression in Neoplasms of the Pancreas: Applications to Diagnostic Pathology (2003)

It seems that, lately, every pathology journal has three or four articles documenting the discovery of another genetic alteration or describing global gene expression in a series of cancers. Although these discoveries provide insight into the biology of neoplasia, it is less clear how they can be quickly and efficiently translated to patient care. This review will use neoplasms of the pancreas as a model and show how recent discoveries of genetic alterations and gene expression patterns can have a significant impact on the diagnosis and even treatment of tumors. Emphasis will be placed on applications that are practical and useful to the daily practice of pathology.
Experimental demonstration of nanosecond-accuracy wireless network synchronization (2015)

Accurate wireless timing synchronization has been an extremely important topic in wireless sensor networks, required in applications ranging from distributed beam forming to precision localization and navigation. However, it is very challenging to realize, in particular when the required accuracy should be better than the runtime between the nodes. This work presents, to our knowledge for the first time, an experimental timing synchronization scheme that achieves a timing accuracy better than 5-ns rms in a network with 4 nodes. The experimental hardware is built from commercially available components and based on software-defined ultra-wideband transceivers. The protocol for establishing the synchronization is based on our recently developed “blink” protocol that can scale from the small network demonstrated here to larger networks of hundreds or thousands of nodes.
Simulation of Valveless Pump Using Pumping Chamber Connected to Elastic Tube (2013)

탄성튜브가 연결된 펌핑 챔버를 이용한 무밸브 펌프를 가상경계방법을 이용하여 수치적으로 연구하였다. 탄성 튜브와 펌핑 챔버 사이의 상호작용으로 인하여 무밸브 펌프 내의 유동이 생성되었으며, 탄성튜브의 스트레칭 계수, 벤딩 계수, 종횡비가 무밸브 펌프의 전체 유량에 미치는 영향을 살펴보았다. 펌프의 메커니즘을 이해하고자, 시간에 따른 탄성 튜브의 움직임과 그에 따른 유동 속도의 변화를 자세히 살펴보았으며, 탄성 튜브의 직경 크기와 펌프의 평균 유량 사이의 관계를 분석하였다.
Landscape of transcriptomic interactions between breast cancer and its microenvironment (2019)

Solid tumours comprise mixtures of tumour cells (TCs) and tumour-adjacent cells (TACs), and the intricate interconnections between these diverse populations shape the tumour's microenvironment. Despite this complexity, clinical genomic profiling is typically performed from bulk samples, without distinguishing TCs from TACs. To better understand TC-TAC interactions, we computationally distinguish their transcriptomes in 1780 primary breast tumours. We show that TC and TAC mRNA abundances are divergently associated with clinical phenotypes, including tumour subtypes and patient survival. These differences reflect distinct responses of TCs and TACs to specific somatic driver mutations, particularly TP53. These data further elucidate how the molecular interplay between breast tumours and their microenvironment drives aggressive tumour phenotypes.
Road of IT Security Standard (2013)

1977年頃，暗号から始まった標準化活動は，各種暗号応用，セキュリティ評価基準，セキュリティマネジメントシステムなど数々の重要標準を生み出した．この延長上で最近のクラウド，M2Mにおいて，進化した形で高機能暗号，機能安全・セキュリティ，ICチップの耐タンパ性，模倣防止技術が重要な役割を演じつつある．
Analytical Performance of Four Portable Gas Chromatographs Under Field Conditions (1990)

A field evaluation of the performance of four portable gas chromatographs was conducted at two field sites, one in the Pacific Northwest (chlorinated solvent contamination) and one in the Desert Southwest (primarily jet fuel contamination). The purpose of the study was to compare the performance of four portable GCs under the same conditions. The gas chromatographs had either electron-capture detectors or photoionization detectors. The study evaluated instrument linearity, instrument detection limits, retention time stabilities, response factor stability, and chromatographic performance. Standards and samples contained 1, 1, 2, 2-tetrachloroethane, trichloroethene, tetrachloroethane, 1, 1, 1-trichloroethane, benzene, toluene, and ethylbenzene. In order to ensure data comparability, the same model wide-bore column and computing integrator were used with each instrument, where possible. Significant differences in the performance of the four models were detected under the specific conditions used for this study. The results indicate the need to fully characterize the performance of portable instruments before field use so that appropriate quality control measures can be planned and implemented based on the performance of a specific analytical system.
Machine learning prediction of enzyme optimum pH (2023)

Abstract The relationship between pH and enzyme catalytic activity, especially the optimal pH (pHopt) at which enzymes function, is critical for biotechnological applications. Hence, computational methods to predict pHopt will enhance enzyme discovery and design by facilitating accurate identification of enzymes that function optimally at specific pH levels, and by elucidating sequence-function relationships. In this study, we proposed and evaluated various machine-learning methods for predicting pHopt, conducting extensive hyperparameter optimization, and training over 11,000 model instances. Our results demonstrate that models utilizing language model embeddings markedly outperform other methods in predicting pHopt. We present EpHod, the best-performing model, to predict pHopt, making it publicly available to researchers. From sequence data, EpHod directly learns structural and biophysical features that relate to pHopt, including proximity of residues to the catalytic center and the accessibility of solvent molecules. Overall, EpHod presents a promising advancement in pHopt prediction and will potentially speed up the development of enzyme technologies.
Toward a Scalable Census of Dashboard Designs in the Wild: A Case Study with Tableau Public (2023)

Dashboards remain ubiquitous artifacts for presenting or reasoning with data across different domains. Yet, there has been little work that provides a quantifiable, systematic, and descriptive overview of dashboard designs at scale. We propose a schematic representation of dashboard designs as node-link graphs to better understand their spatial and interactive structures. We apply our approach to a dataset of 25,620 dashboards curated from Tableau Public to provide a descriptive overview of the core building blocks of dashboards in the wild and derive common dashboard design patterns. To guide future research, we make our dashboard corpus publicly available and discuss its application toward the development of dashboard design tools.
Iterative feature normalization for emotional speech detection (2011)

Contending with signal variability due to source and channel effects is a critical problem in automatic emotion recognition. Any approach in mitigating these effects however has to be done so as to not compromise emotion-relevant information in the signal. A promising approach to this problem has been through feature normalization using features drawn from non-emotional ("neutral") speech samples. This paper considers a scheme for minimizing the inter-speaker differences while still preserving the emotional discrimination of the acoustic features. This can be achieved by estimating the normalization parameters using only neutral speech, and then applying the coefficients to the entire corpus (including emotional set). Specifically, this paper introduces a feature normalization scheme that implements these ideas by iteratively detecting neutral speech and normalizing the features. As the approximation error of the normalization parameters is reduced, the accuracy of the emotion detection system increases. The accuracy of the proposed iterative approach, evaluated across three databases, is only 2.5% lower than the one trained with optimal normalization parameters, and 9.7% higher than the one trained without any normalization scheme.
<title>Fiber optic sensor based on microencapsulated reagents</title> (1993)

The use of irreversible indicating chemistries necessitates a constant supply of reagent to the sensor's tip. In previous work we demonstrated the delivery of reagents incorporated in an ethylene-vinyl acetate copolymer matrix. In this paper we show how a degradable polymer, poly(lactide-glycolide), can be used for sensor preparation. The use of this polymer as a matrix entrapping reagent(s) is described for two different configurations. Sensors are prepared using either composites of dispersed HPTS(1-hydroxy-pyrene-3,6,8-trisulfonate) in polymer layers or microparticles incorporating dyes.
SMS design method in 3D geometry: examples and applications (2004)

The Simultaneous Multiple Surface (SMS) method in 3D geometry is presented. Giving two orthotomic input ray bundles and other two orthotomic output ray bundles, the method provides an optical system with two free-form surfaces that deflects the rays of the input bundles into the rays of the corresponding output bundles and vice versa. In nonimaging applications, the method allows controlling the light emitted by an extended light source much better than single free-form surfaces designs, and also enables the optics contour to be shaped without efficiency losses. The method is expected to find also applications in imaging optics
Optimum biorthogonal DMT systems for multi-service communication (2004)

This paper considers the design of biorthogonal DMT multicarrier transceiver systems supporting multiple services. The supported user services may have differing quality of service (QoS) requirements, quantified in this paper by bit rate and symbol error rate specifications. To reflect their service priorities, different users on the system can be potentially assigned different number of subchannels. Our goal is to minimize the transmitted power given the QoS specifications for the different users, subject to the knowledge of colored interference at the receiver input of the DMT system. In particular we find an optimum bit loading scheme that distributes the bit rate transmitted across the various subchannels belonging to the different users, and subject to this bit allocation, determine an optimum transceiver. This work differs from our prior work where the same number of subchannels were assigned to each user.
Effects of Glutamine, Glucose, and Oxygen Concentration on the Metabolism and Proliferation of Rabbit Adipose-Derived Stem Cells (2006)

The use of adipose-derived stem cells (ASCs) for tissue engineering involves exposing them to metabolically adverse conditions. This study examined the metabolism, proliferation, and viability of ASCs under various oxygen, glucose, and glutamine concentrations to determine how these cells respond to such environments. ASCs were cultured in each of 8 media preparations containing 4.8 or 21.5 mM glucose, and 0, 2, 4, or 6 mM glutamine. The ASCs were cultured under normoxic (20% O(2)) and hypoxic (0.1% O(2)) conditions. Conditioned media were collected and assayed for glucose, glutamine, lactate, pyruvate, and glutamate. Cell proliferation and cell death were measured after 5 days of culture. ASCs remained metabolically active under all culture conditions; however, their proliferation rate was significantly reduced in the absence of glutamine. Hypoxia resulted in increased cell death. ASCs are a viable source of stem cells for tissue engineering purposes, although substantial challenges remain. These cells are able to survive in environments with limited oxygen and glutamine and thus may be able to survive brief periods of limited nutrient transport after implantation.
Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference (2022)

We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a character matrix that considerably reduces homoplasy compared with morphological and nucleotide-based matrices, on both established phylogenies and difficult-to-resolve nodes in the mammalian tree. Champagne provides ample evidence in the form of genomic structural variation to support incomplete lineage sorting and possible introgression in Paenungulata and human-chimp-gorilla which were previously inferred primarily through matrices composed of aligned single-nucleotide characters. Champagne also offers further evidence for Myomorpha as sister to Sciuridae and Hystricomorpha in the rodent tree. Champagne harbors distinct theoretical advantages as an automated method that produces nearly homoplasy-free character matrices on the whole-genome scale.
Effect of Activating Flux on Penetration in ATIG Welding of 316 Stainless Steel (2017)

Tungsten inert gas welding is popular in some industries due to the possibility of obtaining good weld bead surface and high-quality joint without any weld defect. However, compared to many welding processes, shallow penetration of TIG welding hinders its applicability to weld thick components in one pass, thus the productivity is relatively low. An increased depth of penetration can be achieved by Activated TIG (ATIG) welding leading to overall reduction in number of welding passes, and thus increasing productivity. In the present work, attempts were made to find out the optimum flux mixture of SiO and TiO from various ratio of mixtures by carrying out 2 2 bead-on-plate welding on AISI 316 Stainless Steel specimens. From the obtained experimental data, suitable flux ratio was tried to find out giving the highest depth of penetration.
Crystal structures of nucleic acids and their drug complexes (1998)

S. Neidle and C. M. Nunn, Nat. Prod. Rep., 1998, 15, 1 DOI: 10.1039/A815001Y
Data layouts for object-oriented programs (2007)

Object-oriented programs rely heavily on objects and pointers, making them vulnerable to slow downs from cache and TLB misses. The cache and TLB behavior depends on the data layout of objects in memory. There are many possible data layouts with different impacts on performance, but it is not known which perform better. This paper presents a novel framework for evaluating data layouts. The framework both makes implementing many layouts easy, andenables performance measurements of real programs using a product Java virtual machine on stock hardware. This is achieved by sorting objects during copying garbage collection; outside of garbage collection, program performance is solely determined by the data layout that the sort key implements. This paper surveys and evaluates 10 common data layouts with 32 realistic bench mark programs running on 3 different hardware configurations. The results confirm the importance of data layouts for program performance, and show that almost all layouts yield the best performance for some programs and the worst performance for others.
Smart Digital Video Interfaces Solve the Problem of Multiple Standards (1999)

Recent introduction of many new digital high definition video standards has created a challenge for interfacing various types of video equipment. On the same physical interconnections a variety of different video and audio formats can be transported. There are already over 57 new different video formats standardized, and the number will likely continue to grow. — The formats may have any combination of the following parameters: • active raster size (display resolution), • progressive or not, • different vertical rates, • RGB or YUV color space, • different synchronization references, • ancillary data presence and type, • multiple transport links (auto-adjustment of phase) • timing reference signals — Future digital video equipment will incorporate smart interfaces to relief users from the burden of “running around” and manually switching modes of different “boxes”. Smart interfaces will increase productivity of video studios, video databases and such. — This paper describes a computer system (with storage) employing a smart video interface to automate system interaction with the outside video equipment. The paper also explores detailed technical solutions to the smart video interface challenge. Example of “High Definition Video I/O” card from SGI (former Silicon Graphics) is used to illustrate how the right architecture can allow for implementation of various circuits for automatic recognition of video formats. The card received two awards (“NAB 99 editors' pick of show”, and “The Tommy Award” from Millimeter magazine“) and great applause from the video post-production community.
Molecular Recognition of Quadruplex DNA by Quinacridine Derivatives (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Figure S4 from Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy (2023)

&lt;p&gt;Treatment with venetoclax does not result in a reset of the epigenome&lt;/p&gt;
Minisci-Photoredox-Mediated α-Heteroarylation of N-Protected Secondary Amines: Remarkable Selectivity of Azetidines (2018)

The development of a general, mild, and functional-group-tolerant direct functionalization of N-heteroarenes by C-H functionalization with N-protected amines, including azetidines under Minisci-mediated photoredox conditions, is reported. A broad scope of substituted azetidines, including spirocyclic derivatives, and heterocycles were explored. This reaction enables the production of sp3-rich complex druglike structures in one step from unactivated feedstock amines and heterocycles.
Enhanced overall efficiency of GaInN-based light-emitting diodes with reduced efficiency droop by Al-composition-graded AlGaN/GaN superlattice electron blocking layer (2013)

AlxGa1−xN/GaN superlattice electron blocking layers (EBLs) with gradually decreasing Al composition toward the p-type GaN layer are introduced to GaInN-based high-power light-emitting diodes (LEDs). GaInN/GaN multiple quantum well LEDs with 5- and 9-period Al-composition-graded AlxGa1−xN/GaN EBL show comparable operating voltage, higher efficiency as well as less efficiency droop than LEDs having conventional bulk AlGaN EBL, which is attributed to the superlattice doping effect, enhanced hole injection into the active region, and reduced potential drop in the EBL by grading Al compositions. Simulation results reveal a reduction in electron leakage for the superlattice EBL, in agreement with experimental results.
Data Discovery Problem Statement (2020)

If data is the new oil of the 21st century, then we need a
standardized way of locating, capturing, classifying and transforming
this raw data to generate insights and recommendations. Data, like
oil, needs to be discovered and captured in order to be refined and
valuable. While the topic of data discovery can be far reaching, this
document focuses on the problem of actually locating data, throughout
a network of data servers, in a standardized way.
Feasibility and Accuracy of Nasal Alar Pulse Oximetry (2015)

Morey, T. E.*; Rice, M. J.*; Vasilopoulos, T.†; Dennis, D. M.*‡; Melker, R. J.*‡ Author Information