gebhart/patrepeval huggingface dataset:
Supplementary Data from Organic Cation Transporters Modulate the Uptake and Cytotoxicity of Picoplatin, a Third-Generation Platinum Analogue (2023)

Supplementary Data from Organic Cation Transporters Modulate the Uptake and Cytotoxicity of Picoplatin, a Third-Generation Platinum Analogue
Are Very Deep Neural Networks Feasible on Mobile Devices (2016)

In the recent years, the computing power of mobile devices has increased tremendously, a trend that is expected to continue in the future. With high-quality onboard cameras, these devices are capable of collecting large volumes of visual information. Motivated by the observation that processing this video on the mobile device can enable many new applications, we explore the feasibility of running very deep Convolutional Neural Networks (CNNs) for video processing tasks on an emerging class of mobile platforms with embedded GPUs. We find that the memory available in these mobile GPUs is significantly less than necessary to execute very deep CNNs. We then quantify the performance of several deep CNNspecific memory management techniques, some of which leverage the observation that these CNNs have a small number of layers that require most of the memory. We find that a particularly novel approach that offloads these bottleneck layers to the mobile device’s CPU and pipelines frame processing is a promising approach that does not impact the accuracy of these tasks. We conclude by arguing that such techniques will likely be necessary for the foreseeable future despite technological improvements.
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images (2022)

Breast cancer is the most commonly diagnosed cancer and registers the highest number of deaths for women. Advances in diagnostic activities combined with large-scale screening policies have significantly lowered the mortality rates for breast cancer patients. However, the manual inspection of tissue slides by pathologists is cumbersome, time-consuming and is subject to significant inter- and intra-observer variability. Recently, the advent of whole-slide scanning systems has empowered the rapid digitization of pathology slides and enabled the development of Artificial Intelligence (AI)-assisted digital workflows. However, AI techniques, especially Deep Learning, require a large amount of high-quality annotated data to learn from. Constructing such task-specific datasets poses several challenges, such as data-acquisition level constraints, time-consuming and expensive annotations and anonymization of patient information. In this paper, we introduce the BReAst Carcinoma Subtyping (BRACS) dataset, a large cohort of annotated Hematoxylin and Eosin (H&amp;E)-stained images to advance AI development in the automatic characterization of breast lesions. BRACS contains 547 Whole-Slide Images (WSIs) and 4539 Regions Of Interest (ROIs) extracted from the WSIs. Each WSI and respective ROIs are annotated by the consensus of three board-certified pathologists into different lesion categories. Specifically, BRACS includes three lesion types, i.e., benign, malignant and atypical, which are further subtyped into seven categories. It is, to the best of our knowledge, the largest annotated dataset for breast cancer subtyping both at WSI and ROI levels. Furthermore, by including the understudied atypical lesions, BRACS offers a unique opportunity for leveraging AI to better understand their characteristics. We encourage AI practitioners to develop and evaluate novel algorithms on the BRACS dataset to further breast cancer diagnosis and patient care. Database URL: https://www.bracs.icar.cnr.it/.
FtsH Recognizes Proteins with Unfolded Structure and Hydrolyzes the Carboxyl Side of Hydrophobic Residues (2000)

FtsH of Escherichia coli is an essential membrane-integrated ATP-dependent protease. We cloned a gene for an FtsH homolog (T. FtsH) from Thermus thermophilus HB8, expressed it in E. coli, and purified the expressed protein. ATPase activity of T.FtsH was activated by proteins with unfolded structure ( alpha-casein and pepsin), and T.FtsH digested these proteins in an ATP-, Zn(2+)-dependent manner. alpha-Lactalbumin was digested by T.FtsH when it was largely unfolded, but not in its native form. Analysis of the proteolytic products revealed that, in most cases, T.FtsH cleaved the C-terminal side of hydrophobic residues and produced a characteristic set of small peptides (<30 kDa) without releasing a large intermediate. Thus, T.FtsH recognizes the unfolded structure of the proteins and progressively digests them at the expense of ATP. A soluble domain of T.FtsH, which lacked the N-terminal two transmembrane helices, was also prepared but was found to retain neither ATPase nor protease activities. Thus, the membrane segment appeared to be indispensable for these activities of T.FtsH.
Porphyrin-Diones and Porphyrin-Tetraones:  Reversible Redox Units Being Localized within the Porphyrin Macrocycle and Their Effect on Tautomerism (2007)

Porphyrin-2,3-diones and porphyrin-2,3,7,8- and porphyrin-2,3,12,13-tetraones were shown to have a redox-active unit that can function independently of the macrocycle at large. Electroreduction of 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrin-2,3-diones [(P-dione)M] and the corresponding -2,3,12,13-tetraones [L-(P-tetraone)M] and -2,3,7,8-tetraones [C-(P-tetraone)M], where M = 2H, CuII, ZnII, NiII, and PdII was investigated and the products were characterized by ESR and thin-layer UV-visible spectroelectrochemistry. Electrochemical and spectroelectrochemical data show that the first two reductions of the porphyrin-diones and the first three reductions of the porphyrin-tetraones occur at the dione units. This was confirmed by ESR spectra of first reduction products which show that the electron spin is totally localized on a semidione unit, independent of the central metal ion and of the number and location of dione units. ESR spectra of the radical anions derived from free-base porphyrin-2,3-dione [(P-dione)2H] and porphyrin-2,3,12,13-tetraone [L-(P-tetraone)2H] confirm the trans-arrangement of the two inner protons and their location on nonsubstituted pyrrolic rings, thereby maintaining an 18-atom 18-pi electron bacteriochlorin-like aromatic delocalization pathway. The redox unit is not similarly isolated in the corner free-base porphyrin-2,3,7,8-tetraone [C-(P-tetraone)2H]. A one-electron reduction of C-(P-tetraone)2H leads to the formation of a tautomer with trans inner hydrogens with one residing on the N of the ring with the reduced unit as the only detectable product. This process is favorable because it creates a more delocalized 18-atom 18-pi electron aromatic pathway. This result is consistent with the measured redox potentials which show the first reduction of C-(P-tetraone)2H to be substantially easier than (P-dione)2H or L-(P-tetraone)2H.
Consumption of alcoholic beverages and the risk of nasopharyngeal carcinoma: a systematic review and meta‐analysis (2007)

OBJECTIVE: The evidence concerning the influence of alcohol drinking on the risk of nasopharyngeal carcinoma (NPC) has yielded intriguing findings but lacked a clear‐cut interpretation due to inconsistencies. To unify this body of evidence, we performed a systematic review. METHODS: With funding and using a protocol developed by the World Cancer Research Fund (WCRF), 15 bibliographic databases were searched for epidemiological studies that reported a measure of association between alcoholic beverage intake and NPC. There were no language restrictions. Pooled odds ratio (OR) for highest‐vs.‐lowest categories of total alcohol intake was obtained by using a random‐effects model. A dose‐response trend was examined in models using generalized least square estimation. RESULTS: The search identified 11 case‐control studies and 1 cohort study. For total alcohol beverage consumption, the pooled ORs for highest‐vs.‐lowest categories was 1.33 (95% CI: 1.09, 1.62 drinks/week) in 11 case‐control studies. Data from 6 case‐control studies indicated a weak dose‐response trend that was not statistically significant (OR: 1.006; 95% CI: 0.995, 1.017 drinks/week). Fewer data were available to assess the associations between NPC and intake of beer, wine, and spirits. CONCLUSION: Considered in total, total alcoholic intake was associated with a weak increase in risk of NPC in adults.
Genetic characterisation of intestinal spirochaetes and their association with disease (1994)

Multilocus enzyme electrophoresis was used to assess genetic relationships amongst 175 isolates of anaerobic intestinal spirochaetes, including 72 isolates from individuals living in different parts of the world, 102 from pigs and one from a dog. Amongst porcine isolates belonging to the genus Serpulina, a possible new species was identified. All but one of the isolates from man were clustered with the canine isolate and 59 porcine isolates in a distinct group that we have previously called "Anguillina coli". The human and animal spirochaetes in this group had four-to-six axial flagella and most were recovered from individuals with diarrhoea. They included a strain of the so-called "Serpulina jonesii", that was not a true serpulina. These 71 human isolates were distributed into 44 electrophoretic types and had a mean genetic diversity of 0.32. These were further divided into 26 clonal groups. Three of these clones also contained porcine isolates, one of which was strain P43/6/78, the agent of porcine intestinal spirochaetosis. Four of the clones contained human isolates from different sources. One included isolates from Western Australian Aboriginal children and from Italian adults, and the other three contained isolates from Western Australian Aboriginal children and from homosexual males in Sydney, New South Wales. There were no known connections between these human populations. The other spirochaete of human origin was Brachyspira aalborgi, which was distinct from isolates in the genera Serpulina and "Anguillina". Both B. aalborgi and "A. coli" have been associated with human cases of intestinal spirochaetosis.(ABSTRACT TRUNCATED AT 250 WORDS)
Abstract P2-16-01: Discovery of fully human monoclonal antibodies as therapeutic candidates for the treatment of HER2-negative breast cancer (2015)

Abstract Unlike HER2-positive breast cancer, there are limited treatment options for patients diagnosed with triple negative and endocrine resistant HER2-negative breast cancer, and as such HER2-negative breast cancer represents a significant unmet medical need. The goal of this work is to use Theraclone’s proprietary I-STAR platform to mine the memory B cell immune repertoire of breast cancer patients for the discovery of therapeutically relevant monoclonal antibodies (mAbs) and targets that may be exploited as candidates for treatment of HER2-negative breast cancer. Matched serum and PBMC samples were collected from breast cancer patients at multiple clinical sites. The selected patient populations included, but were not limited to, patients who were treatment naïve, those who had received immunotherapy or adjuvant chemotherapy, and patients who had an exceptional clinical response to treatment and/or disease. Serum antibody binding to a diverse panel of 5 well characterized breast cancer-derived cell lines of luminal and basal sub-types was determined. Utilizing this approach, patients with a robust serological profile across multiple breast cancer cell lines were identified and prioritized for memory B cell repertoire analysis via the I-STAR platform. Using a high throughput and miniaturized, multiplex flow cytometry assay, the secreted IgG antibodies from over 85,000 individually enriched and expanded B cell clones were screened for binding to the tumor cell line panel and a large number of positive B cell clones were identified. The screening hits can be binned into several unique binding profiles, many of which were confirmed to be shared across multiple patient samples. Deep sequence analysis of the variable regions of the antibodies produced by the B cell clones demonstrated that several of the screening hits were derived from clonally related B cells; the majority of the screening hits represented antibodies derived from unique B cell clones. A representative set of these antibodies was expressed recombinantly for further in vitro characterization. Citation Format: Christy Boozer, Paul Algate, Aurelio Bonavia, Mark Branum, Po-Ying Chan-Hui, Alison Fitch, Brad Greenfield, Claire Sutherland, Kristine Swiderek. Discovery of fully human monoclonal antibodies as therapeutic candidates for the treatment of HER2-negative breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-16-01.
Formation of hafnium-aluminum-oxide gate dielectric using single cocktail liquid source in MOCVD process (2003)

We demonstrate that a high quality metal organic chemical vapor deposition (MOCVD) HfAl/sub x/O/sub y/ (hereafter HfAlO) dielectric film can successfully be deposited with a wide range of composition controllability between HfO/sub 2/ and Al/sub 2/O/sub 3/ in HfAlO using a single cocktail liquid source HfAl(MMP)/sub 2/(OiPr)/sub 5/. A composition ratio between 45 to 90% of HfO/sub 2/ in HfAlO is achieved by controlling deposition process parameters. The effect of the composition ratio between HfO/sub 2/ and Al/sub 2/O/sub 3/ on the electrical properties of the film is also investigated. The HfAlO film with 90% HfO/sub 2/ (10% Al/sub 2/O/sub 3/), which has minimum sacrifice of K value (around 19), shows a great improvement in thermal stability and significant reduction of interfacial layer growth during subsequent thermal processes, leading to the reduction in leakage current by around 2 orders of magnitude compared to pure HfO/sub 2/ film. The HfAlO film also shows good compatibility with TaN metal gate electrode under high temperature annealing process.
The distributed V kernel and its performance for diskless workstations (1983)

The distributed V kernel is a message-oriented kernel that provides uniform local and network interprocess communication. It is primarily being used in an environment of diskless workstations connected by a high-speed local network to a set of file servers. We describe a performance evaluation of the kernel, with particular emphasis on the cost of network file access. Our results show that over a local network:
SQuBiC1: An integrated control chip for semiconductor qubits (2018)

The Central Institute for Electronic Systems at Forschungszentrum Jülich develops, designs and tests scalable solutions for the control and readout of qubits to be used in future quantum computers. The focus lies on highly integrated system-on-chip (SoC) solutions leveraging state-of-the-art commercial semiconductor technologies.We are working according to the V-model of engineering to approach system solutions in a top-down design and bottom-up implementation. As part of the bottom-up implementation, we designed and layouted a first test chip in a commercial 65nm CMOS process . The chip contains all infrastructure needed to control a GaAs semiconductor qubit. It features a DC-digital-to-analog converter (DC-DAC) that generates the tuning voltages in the range of 0V to +1V to bring the qubit into the operation point. The pulse DAC, running at 250MHz, generates pulses with ± 4mV amplitude to generate gate sequences for operating the qubit. In this presentation, we will describe the chip architecture in detail and show corresponding simulation results.
Correlating stress generation and sheet resistance in InAlN/GaN nanoribbon high electron mobility transistors (2012)

We report the nanoscale characterization of the mechanical stress in InAlN/GaN nanoribbon-structured high electron mobility transistors (HEMTs) through the combined use of convergent beam electron diffraction (CBED) and elastic mechanical modeling. The splitting of higher order Laue zone lines in CBED patterns obtained along the [540] zone axis indicates the existence of a large strain gradient in the c-direction in both the planar and nanoribbon samples. Finite element models were used to confirm these observations and show that a passivating layer of Al2O3 can induce a tensile stress in the active HEMT layer whose magnitude is dependent on the oxide layer thickness, thus, providing important ramifications for device design and fabrication.
Transient Thermal Response of Micro TCD for Identification of Gases (2013)

Abstract not Available.
Minimising the maximum relative regret for linear programmes with interval objective function coefficients (1999)

The minimax relative regret solution to a linear programme with interval objective function coefficients can be found using an algorithm that, at each iteration, solves a linear programme to generate a candidate solution and a mixed integer programme (MIP) to find the corresponding maximum regret. This paper first shows that there exists a regret-maximising solution in which all uncertain costs are at a bound, and then uses this to derive a MIP formulation that maximises the regret of a candidate solution. Computational experiments demonstrate that this approach is effective for problems with up to 50 uncertain objective function coefficients, significantly improving upon the existing enumerative method.
Neonatal Respiratory Care (2012)

Acute respiratory failure caused by different origins continues to be the major etiology of morbidity and mortality in critical neonates. There has been much advancement in neonatal respiratory care, but a few neonates with severe respiratory failure continue to be candidates for extracorporeal membrane oxygenation or survive with chronic lung diseases (CLD). Therefore, searching for ideal respiratory care strategies to reduce the morbidity and mortality rates is crucial for caring critical neonates. The main aim of this special issue was focused on the existing and potential strategies or techniques in neonatal respiratory care. In this special issue, we have invited a few papers that address such issues.

Meconium aspiration syndrome (MAS) is a common cause of severe respiratory failure in term infants. The associations of persistent pulmonary hypertension of newborn (PPHN), pulmonary air leaks, and other morbidities sometimes make the respiratory care a difficult challenge to neonatologists. Three papers address current respiratory care in MAS. In a paper by K. Swarnam et al. they have a detail review on the epidemiology, pathophysiology, and managements in many different views of MAS. In another paper, P. Dargaville focuses on the application of mechanical respiratory supports in MAS, as well as the role of adjunctive respiratory therapies. In a paper, by C. Fischer et al., they demonstrate the epidemiology of MAS in term neonates using a population-based retrospective study for all births from 2000 to 2007 in a French region (Burgundy).

In addition, bronchopulmonary dysplasia (BPD)/chronic lung disease (CLD) continues to be a major cause of neonatal morbidity in spite of significant progress in the treatment of preterm neonates. We have two articles discussing the pharmacologic approaches for prevention and treatment of BPD/CLD. S. Gupta et al. focus on the use of corticosteroids in one paper, and K. Tropea reviews all possible medications and the future potential stem cell therapy in another one.

Furthermore, research papers discussing other important clinical issues in neonatal respiratory care are included. In a paper by S. Rastogi et al., they report their analysis on the factors associated with the successful weaning from nasal continuous positive airway pressure (NCPAP). In a paper by A. Gentili et al., they report their analysis on the duration of preoperative stabilization in predicting outcome of congenital diaphragmatic hernia. In a paper by K. Hole et al., they report the impact of neonatal resuscitation training in neonatal mortality rates in Malawi, Africa.


Mei-Jy Jeng

Tsu F. Yeh

Peter A. Dargaville

Thomas H. Shaffer

Jen-Tien Wung
Hybrid FPGA-accelerated SQL query processing (2013)

Ibex [1] is a novel database storage engine featuring hybrid, FPGA-accelerated query processing. The first prototype of Ibex has been implemented within the open-source MySQL database. In Ibex, an FPGA is inserted into the data path between disk and CPU to act as a query off-loading engine, operating on the stream of data towards the query processor. As a result, the volume of data hitting the CPU is substantially reduced, thereby decreasing energy consumption while increasing performance at the same time.
Cross-Validated Loss-Based Covariance Matrix Estimator Selection in High Dimensions (2021)

The covariance matrix plays a fundamental role in many modern exploratory and inferential statistical procedures, including dimensionality reduction, hypothesis testing, and regression. In low-dimensional regimes, where the number of observations far exceeds the number of variables, the optimality of the sample covariance matrix as an estimator of this parameter is well-established. High-dimensional regimes do not admit such a convenience, however. As such, a variety of estimators have been derived to overcome the shortcomings of the sample covariance matrix in these settings. Yet, the question of selecting an optimal estimator from among the plethora available remains largely unaddressed. Using the framework of cross-validated loss-based estimation, we develop the theoretical underpinnings of just such an estimator selection procedure. In particular, we propose a general class of loss functions for covariance matrix estimation and establish finite-sample risk bounds and conditions for the asymptotic optimality of the cross-validated estimator selector with respect to these loss functions. We evaluate our proposed approach via a comprehensive set of simulation experiments and demonstrate its practical benefits by application in the exploratory analysis of two single-cell transcriptome sequencing datasets. A free and open-source software implementation of the proposed methodology, the cvCovEst R package, is briefly introduced.
Catheter‐tracking FOV MR fluoroscopy (1998)

Recent improvements in intravascular magnetic resonance imaging techniques mandate an accurate method of monitoring the introduction of MR catheter probes into the vessel of interest. For this purpose, a novel imaging protocol and a display method have been designed. First, a roadmap 3D image data set with standard pulse sequences is obtained using an external imaging coil. Subsequently, using very narrow rectangular-FOV fast-spoiled gradient recalled (SPGR), a movie of the percutaneous placement procedure of an MR catheter probe is acquired at a rate of 7.3 frames/second. In this protocol, the probe is used to transmit RF pulses and receive MR signal. A computer program was written for image unwrapping and for displaying the unwrapped movie frames on the roadmap image. In an alternative protocol, the movie frames in two projection angles were acquired in an interleaved fashion. Frames were unwrapped and combined with a 3D roadmap and displayed on a Silicon Graphics workstation equipped with stereovision goggles. Using these methods, percutaneous catheter placement in a phantom and a dog was examined. In conclusion, a new visualization technique for MR catheter placement is proposed. Combining this technique with high resolution intravascular MRI techniques may result in a very useful diagnostic tool for the evaluation of atherosclerosis and other vessel diseases.