gebhart/patrepeval huggingface dataset:
Stack transition artifact removal for cardiac CT using patch-based similarities (2018)

Cardiac CT can be achieved by performing short scans with prospective gating. As the collimation of multi–slice CT scanners generally does not allow for a coverage of the entire heart, sequence scans, also known as step-andshoot, can be used, where irradiation is performed multiple times for varying positions. Each of these short scans yields data, generally with a longitudinal overlap, that can be reconstructed into a sub-volume, or stack. The latter ideally corresponds to the same phase. The issue addressed in this work is irregular motion, such as irregular heart motion. It leads to stacks that do not represent exactly the same volume, resulting in discontinuities at stack transitions when assembling the complete CT volume. We propose a stack transition artifact removal method including a simple symmetric registration approach. Originating from a set of control points in overlap regions between adjacent stacks, the algorithm symmetrically searches for matching sub volumes in the two neighboring stacks, respectively. The offsets to the respective control points of matching sub volumes is used to compute two deformation vector fields that match the two stacks to each other. The deformation vector fields are extended from the overlapping regions in order to maintain smooth and anatomically meaningful images. We validated the method using clinical data sets. By applying a straightforward symmetric registration method to cardiac data, we show that the stack transition artifacts can be addressed in this fashion. The artifact removal was able to considerably improve image quality and constitutes a framework that can be enhanced and expanded on in future.
Retinal progenitor cells release extracellular vesicles containing developmental transcription factors, microRNA and membrane proteins (2018)

A range of cell types, including embryonic stem cells, neurons and astrocytes have been shown to release extracellular vesicles (EVs) containing molecular cargo. Across cell types, EVs facilitate transfer of mRNA, microRNA and proteins between cells. Here we describe the release kinetics and content of EVs from mouse retinal progenitor cells (mRPCs). Interestingly, mRPC derived EVs contain mRNA, miRNA and proteins associated with multipotency and retinal development. Transcripts enclosed in mRPC EVs, include the transcription factors Pax6, Hes1, and Sox2, a mitotic chromosome stabilizer Ki67, and the neural intermediate filaments Nestin and GFAP. Proteomic analysis of EV content revealed retinogenic growth factors and morphogen proteins. mRPC EVs were shown to transfer GFP mRNA between cell populations. Finally, analysis of EV mediated functional cargo delivery, using the Cre-loxP recombination system, revealed transfer and uptake of Cre+ EVs, which were then internalized by target mRPCs activating responder loxP GFP expression. In summary, the data supports a paradigm of EV genetic material encapsulation and transfer within RPC populations. RPC EV transfer may influence recipient RPC transcriptional and post-transcriptional regulation, representing a novel mechanism of differentiation and fate determination during retinal development.
Drought and Salt Tolerance in Plants (2005)

Agricultural productivity worldwide is subject to increasing environmental constraints, particularly to drought and salinity due to their high magnitude of impact and wide distribution. Traditional breeding programs trying to improve abiotic stress tolerance have had some success, but are limited by the multigenic nature of the trait. Tolerant plants such as Craterostigma plantagenium, Mesembryanthemum crystallinum, Thellungiella halophila and other hardy plants could be valuable tools to dissect the extreme tolerance nature. In the last decade, Arabidopsis thaliana, a genetic model plant, has been extensively used for unravelling the molecular basis of stress tolerance. Arabidopsis also proved to be extremely important for assessing functions for individual stress-associated genes due to the availability of knock-out mutants and its amenability for genetic transformation. In this review, the responses of plants to salt and water stress are described, the regulatory circuits which allow plants to cope with stress are presented, and how the present knowledge can be applied to obtain tolerant plants is discussed.
Zyflamend®, a Unique Herbal Preparation With Nonselective OX Inhibitory Activity, Induces Apoptosis of Prostate Cancer Cells That Lack COX-2 Expression (2005)

Cyclooxygenase (COX) inhibitors have suppressive effects on several types of cancer cells including prostate cancer. In this study, we considered the potential COX-inhibitory activity of a unique anti-inflammatory herbal preparation (Zyflamend; New Chapter, Inc., Brattleboro, VT) and analyzed its effects on the human prostate cancer cell line LNCaP. COX inhibitory activity of Zyflamend was determined by a spectrophotometric-based assay using purified ovine COX-1 and COX-2 enzymes. Effects of Zyflamend on LNCaP cell growth and apoptosis in vitro were assessed by cell counting, Western blot detection of poly ADP-ribose polymerase (PARP) cleavage, and measurement of caspase-3 activity in treated and control cell extracts. Western blotting techniques were conducted to determine the effects of this herbal preparation on the expression of the cell signaling proteins, p21, androgen receptor (AR), phospho-protein kinase C (pPKC)(alpha/beta), and phospho (p)Stat3. The phospohorylation status of several signal transduction phosphoproteins was profiled using a high-throughput phosphoprotein screening assay in treated cells and compared to controls. Zyflamend dramatically decreased COX-1 and COX-2 enzymatic activity. Elevated p21 expression coincided with attenuated cell growth following treatment of LNCaP cells with Zyflamend. PARP cleavage fragments were evident, and caspase-3 activity was upregulated over the control indicating the ability of Zyflamend to induce apoptosis of these cells. Androgen receptor expression levels declined by 40%, and decreases were observed in the active forms of Stat3 and PKC(alpha/beta) in Zyflamend-treated LNCaP cells. Zyflamend inhibited both COX-1 and COX-2 enzymatic activities, suppressed cell growth, and induced apoptosis in LNCaP cells. However, our data suggests that the effects are likely due to COX-independent mechanisms potentially involving enhanced expression of p21 and reduced expression of AR, pStat3, and pPKC(alpha/beta).
A cross-jurisdictional research collaboration aiming to improve health outcomes in the tropical north of Australia (2021)

Can equitable health outcomes across Australia be provided by increasingly urban-dominated populations? The Australian HOT North (Improving Health Outcomes in the Tropical North) program has tackled the increasing urban-rural/remote health divide by focusing on three components of the health research ecosystem - researcher retention and recruitment, researcher-practitioner collaborations, and knowledge transfer by forming cross-jurisdictional and multi-disciplinary networks and delivering on-country knowledge translation. We propose that a more widespread implementation of locally-designed research and practice, embedded alongside programs that strengthen cross-jurisdictional networks, would increase health equity in rural and remote areas.
MicroRNAs as Biomarkers for Clinical Features of Lung Cancer (2012)

Each year about 1.4 million people die from lung cancer worldwide. Despite efforts in prevention, diagnosis and treatment, survival rate remains poor for this disease. This unfortunate situation is largely due to the fact that a high proportion of cases are diagnosed at advanced stages, highlighting the great need for identifying new biomarkers in order to improve early diagnosis and treatment. Recent studies on microRNAs have not only shed light on their involvement in tumor development and progression, but also suggested their potential utility as biomarkers for subtype diagnostics, staging and prediction of treatment response. This review article summarizes the impact of microRNAs on lung cancer biology, and highlights their role in the detection and classification of lung cancer as well as direct targets for drug development.
Table S1 from Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer (2023)

&lt;p&gt;Supplemental Table S1 Patient characteristics for the National Lung Screening Trial (NLST) and The Cancer Genome Atlas (TCGA) datasets.&lt;/p&gt;
Sensory and Motor Peripheral Nerve Function and Lower‐Extremity Quadriceps Strength: The Health, Aging and Body Composition Study (2009)

Reduced sensory and motor peripheral nerve function is related to poorer lower extremity strength in older adults, suggesting a mechanism for the relationship with lower extremity disability.
Supplementary Figure 2 from SYD985, a Novel Duocarmycin-Based HER2-Targeting Antibody–Drug Conjugate, Shows Antitumor Activity in Uterine Serous Carcinoma with HER2/Neu Expression (2023)

&lt;p&gt;Exposure of all nine cell lines to scalar concentrations of ADC for a total of 6 days. IC50 dose response curves of SYD985, T-DM1 and ADC isotype control in all 9 primary USC cell lines with differential HER2 expression tested in vitro (i.e., three with HER2 3+ expression, two with HER2 2+ expression and four with HER2 1+ expression) at 6 days (ie, 144 hrs).&lt;/p&gt;
Cytochrome c551 Is a Mediator of Electron Transfer between Copper-Containing Nitrite Reductase and Azurin in a Denitrifying Bacterium, Achromobacter xylosoxidans (2009)

Abstract Cu-containing nitrite reductase from a denitrifying bacterium, Achromobacter xylosoxidans GIFU1051 (the organism formerly known as Alcaligenes xylosoxidans), can accept an electron from three possible electron donors (cytochrome c551 and two azurins). We have kinetically demonstrated that cytochrome c551 functions as a mediator in the electron flow processes between the enzyme and two azurins.
Japan's Income Tax Base: Comparison with Other Countries and Estimation of Tax Reform (2014)

This paper shows that Japan’s income tax base is eroded mainly by the employment income deduction and social security benefits/contributions not being included in the tax base, through comparison with other countries, and how it is possible to increase income tax revenue by correcting these deductions with a simple estimation using tax affair statistics. Firstly, we re-estimate the trend in Japan’s income tax base presented in Morinobu and Nakamoto (2013), reflecting the revision of the benchmark year and retroactive adjustment of SNA. Even though the trend was adjusted downward by 2 or 3%, reflecting the downward adjustment of household receipts, the main causes of the erosion are the deductions for employment income and social security benefits/contributions under Japan’s aging society, in the same way as mentioned in Morinobu and Nakamoto (2013). These features of Japan’s income tax system are confirmed by both comparisons with the macro-estimated income tax base in the U.S. and with more-easily estimated income tax base of the average income class household in the U.S. and other European countries. Recently, the significance of one of the purposes of the employment income deduction, the adjustment to other incomes, has been decreasing, so it is necessary to review the employment income deduction to confine the feature to the deduction for approximate work-related costs. This paper estimates the amounts of increased tax revenue under the assumed reform in the employment income deduction. Tax revenue will increase 50%, with the reform in the employment income deduction, and additionally increase 10% with the extra reform in the deduction for the social security contributions. In short, it’s useful to review the employment income deduction to restore the income tax revenue, especially of the low and middle income brackets.
Study of the fabrication process of Bragg gratings in channel waveguides using ultrafast radiation and the phase mask method (2007)

A study of the capability of the Bragg grating writing method using infrared radiation and a phase mask to inscribe Bragg gratings structures in channel waveguides was performed using as a physical model D-shaped silica fibers. Experiments made with different radiation intensities and focusing arrangements produced surface structure damage of the waveguide during Bragg grating inscription in the D-fiber core. An evaluation of the surface damage intensity threshold and the exposure conditions required to avoid it is presented.
Properties of Amorphous Silicon Nitride Prepared at High Deposition Rate (1985)

A high deposition rate of more than 2.2 nm/s was achieved for hydrogenated amorphous silicon nitride film by applying the substrate tuning method to glow-discharge decomposition of SiH 4 +NH 3 . The atomic ratio N/Si (1.1±0.1) in the film is nearly constant, irrespective of the increase of deposition rate. The valence-electron density and atomic density increase and buffered HF etch rate decreases with deposition rate. This high rate deposition method improves density in amorphous silicon nitride films.
Drying of Ammonium Nitrate Prepared from a Melt (1968)

水分を約5%含有する融液から固化させた硝酸アンモニウム( 溶融硝安) の乾燥と相転移およびオクタデシルアミン(ODA)添加の関連について, 熱天秤, DTA ,顕微鏡観察により調べた。溶融硝安の乾燥過程には誘導時間があり, それは50℃以下でより以上で長いが, これは相転移がからんでくるためである。すなわち, 融液が固化する過程で試料の周辺部から結晶化が起こりこれが皮膜となって乾燥を妨げる。しかしII→III転移が起こるとこの皮膜が破壊され乾燥が始まる。溶融硝安を降温する場合II→III転移は約80℃から48.5℃までの広い範囲で生起し, 一般に大きくかつ一定していない遅れ( 誘導時間) を伴う。しかし48.5℃以下に急冷した場合には遅れはない。つぎにODAを添加した場合は, 結晶皮膜は不完全で乾燥は相転移と無関係に進行し, 乾燥速度も大きい。ODAの添加効果は粉末硝安の乾燥においてもみられるが,その効果はODAが硝安結晶に吸着し,結晶成長や結晶粒間の結合を妨げることによるものとみられる。
The Pathfinder System (1989)

We review highlights of our research on Pathfinder, a decision-theoretic expert system for hematopathology diagnosis. We have developed techniques for efficiently acquiring, representing, and reasoning with uncertain biomedical knowledge. Specifically, we have developed a methodology for coping with complex dependencies among findings and disease in pathology. The methodology includes an extension of the belief-network representation called similarity networks. Using this methodology, we have constructed a large probabilistic knowledge base for the domain of lymph-node pathology. We have also developed techniques for improving the clarity of explanations through the use of human-oriented abstractions. Finally, we have conducted a formal evaluation of Pathfinder's diagnostic accuracy.
Discrete nuclear elastic scattering effects in Cat-D and D-3He fusion plasmas (1984)

The effects of Nuclear Elastic Scattering (NES) on the properties of Cat-D and D-3He plasmas are investigated, with special attention given to the discrete nature of NES. A space-independent, linear multi-group method is used for the study. It is found that NES can significantly reduce the nr requirements for plasma ignition; for plasmas characterized by relatively large cyclotron radiation losses, this reduction can exceed 50%. In addition, the treatment of the discrete NES behaviour is shown to be essential for an accurate prediction of the superthermal ion distribution functions.
Electro-Optical Polarimetric Imaging System for Characterization of Resident Space Objects (2015)

The design, calibration, and testing of an automated polarimetric imaging system aimed at developing efficient and reliable optical polarimetric characterization techniques of resident space objects, with emphasis on satellite space materials, are introduced. The presented electrooptical imaging polarimeter system exhibits a high degree of accuracy and repeatability. The system’s accuracy is investigated using test materials of well-known optical properties. The outcome of this study indicates that the operational design principles of the optical polarimetric system may prove extremely useful in characterizing remote manmade materials commonly used in space.
Scaling analog circuits (2013)

Analog circuits perform critical operations in any modern integrated circuit. Digital integrated circuits require analog circuits for logic or I/O clock generation, as well as for temperature monitoring or supply regulation. In mixed signal products, analog circuits perform the critical translation of information from the physical (analog) world to the digital world of ones and zeros. Analog-to-digital converters are typically preceded by signal conditioning circuits, including filtering and amplification, while digital-to-analog conversion needs to be followed by some form of analog signal conditioning.
Magnetic Fe@FeOx, Fe@C and α-Fe2O3 Single-Crystal Nanoblends Synthesized by Femtosecond Laser Ablation of Fe in Acetone (2018)

There are few reports on zero-field-cooled (ZFC) magnetization measurements for Fe@FeO<sub>x</sub> or FeO<sub>x</sub> particles synthesized by laser ablation in liquids (LAL) of Fe, and the minimum blocking temperature (T<sub>B</sub>) of 120 K reported so far is still much higher than those of their counterparts synthesized by chemical methods. In this work, the minimum blocking temperature was lowered to 52 K for 4⁻5 nm α-Fe₂O₃ particles synthesized by femtosecond laser ablation of Fe in acetone. The effective magnetic anisotropy energy density (K<sub>eff</sub>) is calculated to be 2.7⁻5.4 × 10⁵ J/m³, further extending the K<sub>eff</sub> values for smaller hematite particles synthesized by different methods. Large amorphous-Fe@α-Fe₂O₃ and amorphous-Fe@C particles of 10⁻100 nm in diameter display a soft magnetic behavior with saturation magnetization (M<sub>s</sub>) and coercivities (H<sub>c</sub>) values of 72.5 emu/g and 160 Oe at 5 K and 61.9 emu/g and 70 Oe at 300 K, respectively, which mainly stem from the magnetism of amorphous Fe cores. Generally, the nanoparticles obtained by LAL are either amorphous or polycrystalline, seldom in a single-crystalline state. This work also demonstrates the possibility of synthesizing single-crystalline α-Fe₂O₃ hematite crystals of several nanometers with (104), (113), (116) or (214) crystallographic orientations, which were produced simultaneously with other products including carbon encapsulated amorphous Fe (a-Fe@C) and Fe@FeO<sub>x</sub> core-shell particles by LAL in one step. Finally, the formation mechanisms for these nanomaterials are proposed and the key factors in series events of LAL are discussed.
AT1 Receptor Antagonist Combats Oxidative Stress in the JGA of the SHR (2000)

24 The tubuloglomerular feedback (TGF) responses of the SHR are under exaggerated regulation by angiotensin II (Ang II) type 1 receptors (AT 1 -R). Since AT 1 -R enhance oxygen radical (O 2 - ) generation, we tested the hypothesis that the exaggerated TGF was due to a diminished blunting by macula densa (MD)-derived nitric oxide (NO) because of excessive AT 1 -R-dependent generation of O 2 - . Groups (n=6-9) of SHR and control WKY rats received vehicle (Veh), the AT 1 -R antagonist candesartan (Cand; 3 mg·kg -1 ·d -1 ) or non-specific therapy with hydralazine + hydrochlorothiazide + reserpine (HHR) for two weeks. Compared to WKY, the elevated mean arterial pressure of SHR (WKY: 125±2 vs. SHR: 163±9 mmHg; p 2 - , tempol (a membrane-permeable superoxide dismutase mimetic) was perfused into the efferent arteriole. During tempol, SHR given vehicle or HHR had a much increased response to blockade of nNOS with 7-NI (ΔTGF with 7-NI during tempol: Veh, +6.3±1.0 and HHR, +4.5±0.8 mmHg; p 2 - . In contrast, the TGF response to 7-NI in SHR given Cand was unaffected by tempol (ΔTGF with 7-NI during tempol: +2.9±0.9; ns compared to no tempol). In conclusion, TGF responses of SHR are exaggerated due to effects of hypertension and AT 1 -R. AT 1 -R blockade specifically diminishes oxidative stress and restores NO signaling in the JGA of the SHR.
vSQL: Verifying Arbitrary SQL Queries over Dynamic Outsourced Databases. (2017)

Cloud database systems such as Amazon RDS or Google Cloud SQLenable the outsourcing of a large database to a server who then responds to SQL queries. A natural problem here is to efficiently verify the correctness of responses returned by the (untrusted) server. In this paper we present vSQL, a novel cryptographic protocol for publicly verifiable SQL queries on dynamic databases. At a high level, our construction relies on two extensions of the CMT interactive-proof protocol [Cormode et al., 2012]: (i) supporting outsourced input via the use of a polynomial-delegation protocol with succinct proofs, and (ii) supporting auxiliary input (i.e., non-deterministic computation) efficiently. Compared to previous verifiable-computation systems based on interactive proofs, our construction has verification cost polylogarithmic in the auxiliary input (which for SQL queries can be as large as the database) rather than linear. In order to evaluate the performance and expressiveness of our scheme, we tested it on SQL queries based on the TPC-H benchmark on a database with 6 million rows and 13 columns. The server overhead in our scheme (which is typically the main bottleneck) is up to 120 times lower than previousapproaches based on succinct arguments of knowledge (SNARKs), and moreover we avoid the need for query-dependent pre-processing which is required by optimized SNARK-based schemes. In our construction, the server/client time and the communication cost are comparable to, and sometimessmaller than, those of existing customized solutions which only support specific queries.
SOI gated resistor: CMOS without junctions (2009)

We report the fabrication of junctionless SOI MOSFETs. Such devices greatly simplify processing thermal budget and behave as regular multigate SOI transistors.
A Study on Application of Convolutional Code in LoRa PHY (2020)

최근 들어 IoT(internet of things) 통신을 위한 비면허 대역의 저전력 광대역(LPWA: low power wide area) 네트워크 기술 개발이 활발히 진행되고 있으며, 이 중에서도 LoRa(long range) 시스템은 지속적으로 응용 분야를 넓혀가고 있다. LoRa 시스템의 MAC 계층 규격은 표준화되어 공개되어 있으나, LoRa 시스템의 물리계층 규격은 Semtech이 특허권을 가지고 있어서 세부 내용이 완벽히 공개되어 있지는 못하다. 이에 본 논문에서는 페이딩 환경에서의 LoRa 물리계층의 성능을 분석해 보고자 한다. 우선 페이딩 환경에서의 LoRa 변조(LoRa modulation)에 대한 SER과 BER의 상관관계를 컴퓨터 모의실험을 통해 분석할 것이다. 또한 기존의 (8,4) hamming 코드 대신 동일한 코딩률을 갖는 코딩률 1/2 길쌈부호(1/2 rate convolutional code)를 적용할 경우, LoRa 물리계층의 성능 이득을 비교하고자 한다.
Otx2-PNN Interaction to Regulate Cortical Plasticity (2016)

The ability of the environment to shape cortical function is at its highest during critical periods of postnatal development. In the visual cortex, critical period onset is triggered by the maturation of parvalbumin inhibitory interneurons, which gradually become surrounded by a specialized glycosaminoglycan-rich extracellular matrix: the perineuronal nets. Among the identified factors regulating cortical plasticity in the visual cortex, extracortical homeoprotein Otx2 is transferred specifically into parvalbumin interneurons and this transfer regulates both the onset and the closure of the critical period of plasticity for binocular vision. Here, we review the interaction between the complex sugars of the perineuronal nets and homeoprotein Otx2 and how this interaction regulates cortical plasticity during critical period and in adulthood.