gebhart/patrepeval huggingface dataset:
The Lithuanian reference genome LT1 - a human de novo genome assembly with short and long read sequence and Hi-C data (2021)

Abstract We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly constructed using 57× of ultra-long nanopore reads and 47× of short paired-end reads. We also utilized 72 Gb of Hi-C chromosomal mapping data to maximize the assembly’s contiguity and accuracy. LT1’s contig assembly was 2.73 Gbp in length comprising of 4,490 contigs with an N50 value of 13.4 Mbp. After scaffolding with Hi-C data and extensive manual curation, we produced a chromosome-scale assembly with an N50 value of 138 Mbp and 4,699 scaffolds. Our gene prediction quality assessment using BUSCO identify 89.3% of the single-copy orthologous genes included in the benchmarking set. Detailed characterization of LT1 suggested it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,000 short indels, and 12,330 large structural variants. These data are shared as a public resource without any restrictions and can be used as a benchmark for further in-depth genomic analyses of the Baltic populations.
A 2.7 V CMOS IF transceiver for PHS application (2002)

This paper describes a single chip 2.7 V 248.5 MHz IF transceiver including VCO, PLL and a complete voice codec for personal handy phone system (PHS). The IC is implemented in a 0.6-/spl mu/m CMOS process. It achieves a receive sensitivity of -86 dBV, 1 dB compression point of -9 dBV and 32 dB image rejection. This circuit consumes 24 mA in the receive mode, 26 mA in the transmit mode, and 4.5 mA in the voice codec.
Ability to Predict New-Onset Psychological Distress Using Routinely Collected Health Data: A Population-Based Cohort Study of Women Diagnosed With Breast Cancer (2018)

<b>Objectives:</b> The primary objective of this study was to identify the predictors of new-onset psychological distress available in routinely collected administrative health databases for women diagnosed with breast cancer. The secondary objective was to explore whether the predictors vary based on the period of cancer care. <b>Methods:</b> A population-based cohort study followed 16,495 female patients with newly diagnosed breast cancer who did not experience psychological distress during the 14 months before breast cancer surgery. The incidence of psychological distress was reported overall and by type of mental health problem. Time-varying Cox proportional hazards models were developed to identify predictors of new-onset psychological distress during 2 key periods of cancer care: (1) hospital-based treatment during which women undergo treatment with breast surgery, chemotherapy, and/or radiation, and (2) 1-year transitional survivorship when women begin follow-up care. <b>Results:</b> The incidence of psychological distress was 16% within each period. Anxiety was present in 85.1% and 65.5% of new cases during hospital-based treatment and transitional survivorship, respectively. Predictors during both periods were younger age, receipt of axillary lymph node dissection, rheumatologic disease, and baseline menopausal symptoms, as well as new opioid dispensations, emergency department visits, and hospital contacts that occurred during follow-up. Other predictors varied based on the period of cancer care. More advanced breast cancer and type of treatment were associated with onset of psychological distress during hospital-based treatment. Psychological distress during transitional survivorship was predicted by diagnosis of localized breast disease, shorter duration of hospital-based treatment, receipt of additional hospital-based treatment in survivorship, and newly diagnosed comorbidities or symptoms. <b>Conclusions:</b> This study identified the predictors of new-onset psychological distress available in routinely collected administrative health databases, and showed how predictors change between hospital-based treatment and transitional survivorship periods. The results highlight the importance of developing predictive models tailored to the period of cancer care.
Robust heavy-ion-beam illumination against a direct-drive-pellet displacement in inertial confinement fusion (2005)

Nonuniformity of heavy-ion-beam (HIB) illumination is one of key issues in the HIB inertial confinement fusion (ICF): implosion symmetry should be less than a few percent in order to compress a fuel sufficiently and release fusion energy effectively. In this paper a new HIB illumination scheme is presented in order to realize a robust illumination scheme against a displacement of a direct-driven fuel pellet in an ICF reactor. It is known that the HIB illumination nonuniformity is sensitive to a little pellet displacement from a reactor chamber center; a pellet displacement of only 50–100μm was tolerable in the conventional HIB illumination schemes. In this paper by three-dimensional computer simulations a new robust HIB illumination scheme was found, in which a 200–300μm displacement is allowed.
Faculty Opinions recommendation of GEP100 links epidermal growth factor receptor signalling to Arf6 activation to induce breast cancer invasion. (2008)

Epidermal growth factor (EGF) receptor (EGFR) signalling is implicated in tumour invasion and metastasis. However, whether there are EGFR signalling pathways specifically used for tumour invasion still remains elusive. Overexpression of Arf6 and its effector, AMAP1, correlates with and is crucial for the invasive phenotypes of different breast cancer cells. Here we identify the mechanism by which Arf6 is activated to induce tumour invasion. We found that GEP100/BRAG2, a guanine nucleotide exchanging factor (GEF) for Arf6, is responsible for the invasive activity of MDA-MB-231 breast cancer cells, whereas the other ArfGEFs are not. GEP100, through its pleckstrin homology domain, bound directly to Tyr1068/1086-phosphorylated EGFR to activate Arf6. Overexpression of GEP100, together with Arf6, caused non-invasive MCF7 cells to become invasive, which was dependent on EGF stimulation. Moreover, GEP100 knockdown blocked tumour metastasis. GEP100 was expressed in 70% of primary breast ductal carcinomas, and was preferentially co-expressed with EGFR in the malignant cases. Our results indicate that GEP100 links EGFR signalling to Arf6 activation to induce invasive activities of some breast cancer cells, and hence may contribute to their metastasis and malignancy. PMID: 18084281
Dynamic Analysis and Structural Safety Evaluation of the Cabinet of a Reactor Safety System (2005)

Responses of the cabinet of the reactor safety system under seismic leadings are analyzed, its dynamic characteristics and structural reliability being evaluated. Analyzed natural frequencies are compared with those measured from a resonance test. Structural safety of the cabinet is evaluated in consideration of the required response spectrums of the operation-base and safe-shutdown earthquakes. Transient responses of the cabinet are analyzed with input ground acceleration measured during the seismic test, accelerations being extracted at the locations of the main internal parts. The transient responses are compared with those from the seismic test, favorable results being shown.
Back to the future (panel session) (2000)

Functional programming, AI, patterns, OO, structured programming - they were promising, and yet they seem to have failed to deliver. Did we lose interest too soon? Is the best too good for our industry? Is there “a” best for our industry or is our endless search for the silver bullet driving us? Do we want the “best” to (again) be a popular goal? How?
Convolutional neural networks: an overview and application in radiology (2018)

Convolutional neural network (CNN), a class of artificial neural networks that has become dominant in various computer vision tasks, is attracting interest across a variety of domains, including radiology. CNN is designed to automatically and adaptively learn spatial hierarchies of features through backpropagation by using multiple building blocks, such as convolution layers, pooling layers, and fully connected layers. This review article offers a perspective on the basic concepts of CNN and its application to various radiological tasks, and discusses its challenges and future directions in the field of radiology. Two challenges in applying CNN to radiological tasks, small dataset and overfitting, will also be covered in this article, as well as techniques to minimize them. Being familiar with the concepts and advantages, as well as limitations, of CNN is essential to leverage its potential in diagnostic radiology, with the goal of augmenting the performance of radiologists and improving patient care. KEY POINTS: • Convolutional neural network is a class of deep learning methods which has become dominant in various computer vision tasks and is attracting interest across a variety of domains, including radiology. • Convolutional neural network is composed of multiple building blocks, such as convolution layers, pooling layers, and fully connected layers, and is designed to automatically and adaptively learn spatial hierarchies of features through a backpropagation algorithm. • Familiarity with the concepts and advantages, as well as limitations, of convolutional neural network is essential to leverage its potential to improve radiologist performance and, eventually, patient care.
Gapless assembly of maize chromosomes using long read technologies (2020)

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We used long read technologies and an optical map based approach to produce a maize genome assembly composed of only 63 contigs. The B73-Ab10 genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), multiple highly repetitive centromeres and heterochromatic knobs, and 53 Mb of the Ab10 meiotic drive haplotype.
PSIII-4 Determining the Efficacy and Safety of Differing Caliber/Ammunition Combinations for the Humane Euthanization and Subsequent Mass Depopulation of Market Weight Pigs (2021)

Abstract The objective of this proof of concept exercise was to validate a field applicable methodology designed to objectively assess the multiple caliber/ammunition combinations available for the safe and humane euthanization of market weight pigs during mass depopulation events. Heads of an equal number of barrows and gilts (n = 64) were randomly assigned to one of four caliber/ammunition combinations consisting of the .22 LR, .22 Mag, 0.38 Special, and 9mm. Fully jacketed (FMJ) ammunition was discharged from each of four unique firearms while ensuring that the distance from the muzzle to the forehead was consistent. The MIXED procedure of SAS was used to test the fixed effects of sex and caliber. No differences in skull thickness existed between sex (P = 0.32) or caliber/ammunition combination (P = 0.34). There was no difference in entrance wound diameter between the .38 Special and the 9mm (P = 0.15) yet the entrance wound diameter of the .38 Special and 9mm was larger than both the .22 LR and .22 Mag, respectfully (P &amp;lt; 0.0001). The 9mm bullets traveled further into the ballistic gel (P &amp;lt; 0.0001) and the furthest total distance (P &amp;lt; 0.0001). Bullets from the .38 Special traveled further into the ballistic gel and a further total distance than both the .22 LR and .22 Mag (P &amp;lt; 0.0001). There was no difference in the measurable trauma area of the brain for the 9mm bullets compared to .38 Special bullets (P = 0.83). The measurable trauma area of the brain was greater for the 9mm and .38 Special bullets when compared to both the .22 LR and .22 Mag (P &amp;lt; 0.0001). In conclusion, the efficacy and safety of the multiple caliber/ammunition combinations available for use in the euthanization of market weight pigs can be objectively quantified, replicated, and reported.
The Morse lens (2020)

In this letter, we find that Morse potential (proposed about 90 years ago) could be connected to Coulomb potential (or Newton potential) and harmonic potential (or Hooke potential) by conformal mappings. We thereby design a new conformal lens from Morse potential, Eaton lens and Luneburg lens and propose a series of generalized Eaton/Luneburg lenses. We find that this Morse lens is a perfect self-focusing asymmetric lens, which differs from Mikaelian lens. Our theory provides a new insight to Morse potential and other traditional potentials and revisits their classical applications on designing lenses.
Nitric oxide production in islets from nonobese diabetic mice: aminoguanidine-sensitive and -resistant stages in the immunological diabetic process. (1993)

The role of nitric oxide (NO.) in the development of immunologically induced diabetes was examined. Transfer of spleen cells obtained from diabetic female nonobese diabetic (NOD) mice to nondiabetic irradiated males induced diabetes 11-13 days after transfer. Islets isolated from recipient male mice produced NO. in a time-dependent fashion. The production of nitrite was initially detected at day 6 after transfer, with increasing levels by days 9 and 13. Under similar conditions glucose-induced insulin secretion by isolated NOD mouse islets was irreversibly reduced by approximately 40% at days 6, 9, and 13 after transfer of spleen cells. The number of islets harvested per pancreas by the 9th and 13th day after transfer was decreased by 20-25% as compared to controls. Treatment of male NOD mice with aminoguanidine, an inhibitor of the inducible form of NO. synthase, reduced the production of NO. in islets and delayed the development of diabetes by 3-8 days. The temporary inhibition by aminoguanidine was dependent on both inhibitor concentration and number of spleen cells transferred. These results indicate that NO. is produced in NOD islets as a result of an immunological diabetogenic process and suggests a role of this compound in the immunological diabetic process.
Cardiac and Noncardiac Disease Burden and Treatment Effect of Sacubitril/Valsartan (2021)

Domains of disease burden are clinically relevant features that influence the prognosis and treatment of patients with HF. The therapeutic benefits of sacubitril/valsartan vary according to the balance of components of disease burden, across different ranges of left ventricular ejection fraction.
Characterization of the Human Small‐Ribosomal‐Subunit Proteins by N‐Terminal and Internal Sequencing, and Mass Spectrometry (1996)

Reverse-phase HPLC was used to fractionate 40S ribosomal proteins from human placenta. Application of a C4 reverse-phase column allowed us to obtain 27 well-resolved peaks. The protein composition of each chromatographic fraction was established by two-dimensional polyacrylamide gel electrophoresis and N-terminal sequencing. N-terminally blocked proteins were cleaved with endoproteinase Lys-C, and suitable peptides were sequenced. All sequences were compared with those of ribosomal proteins available from data bases. This allowed us to identify all proteins from the 40S human ribosomal subunit in the HPLC elution profile. By matrix-assisted laser-desorption ionization mass spectrometry the masses of the 40S proteins were determined and checked for the presence of post-translational modifications. For several proteins differences to the deduced sequences and the calculated masses were found to be due to post-translational modifications.
Induction of Transgene-Specific Cytotoxic T Lymphocyte Responses After Transplantation of Gene-Modified CD34 + Cells Despite Nonablative Immunosuppressive Conditioning (2007)

In previous studies we showed that low-dose irradiation and immunosuppression with cyclosporine and mycophenolate mofetil prolonged in vivo persistence of gene-modified T cells but was unable to induce tolerance. We hypothesized that the lack of sustained antigen presentation because of the limited life span of the infused T cells might be responsible for the lack of tolerance induction. Thus, we examined whether tolerance could be induced by infusion of long-lived stem cells. Two baboons were transplanted with YFP/neo-transduced CD34+ cells. The transgene-marked cells disappeared completely within 5 weeks and CD8+ transgene-specific cytotoxic T lymphocytes were detected in both animals. Thus, this nonablative conditioning regimen did not provide sufficient immunosuppression for the induction of tolerance after infusion of gene-modified CD34+ cells.
Monoclonal antibody TGN1412 trial failure explained by species differences in CD28 expression on CD4 + effector memory T‐cells (2010)

It is likely that activation of CD4+ effector memory T-cells by TGN1412 was responsible for the cytokine storm. Lack of CD28 expression on the CD4+ effector memory T-cells of species used for pre-clinical safety testing of TGN1412 offers an explanation for the failure to predict a 'cytokine storm' in humans.
Plasma-Assisted Biological Macromolecular Crystallization (2011)

Improvement in the crystallization probability of biological macromolecules by plasma irradiation is demonstrated with lysozymes from hen egg whites. This novel technique of "plasma-assisted biological macromolecular crystallization" is readily carried out with a relatively simple apparatus, and is likely to become a powerful tool in discerning the three-dimensional structure of such macromolecules.
Error elimination ECC by horizontal error detection and vertical-LDPC ECC to increase data-retention time by 230% and acceptable bit-error rate by 90% for 3D-NAND flash SSDs (2018)

Cross Error Elimination (XEE) ECC with Horizontal Error Detection (HED) and Vertical-LDPC (V-LDPC) is proposed to extend the data-retention lifetime of 3D-TLC NAND flash-based SSD. HED improves the error correction capability of LDPC ECC by evaluating the error bits in the horizontal direction which means the column direction. Moreover, V-LDPC improves the worst reliability in each WL in the vertical row direction through three (Upper/Middle/Lower) pages. This paper investigates the reliability improvement of 3D-TLC NAND flash memory by XEE ECC. As a result, the data-retention lifetime and the acceptable bit-error rate (BER) are extended by 230% and 90%, respectively.
SSRIs target prefrontal to raphe circuits during development modulating synaptic connectivity and emotional behavior (2018)

Antidepressants that block the serotonin transporter, (Slc6a4/SERT), selective serotonin reuptake inhibitors (SSRIs) improve mood in adults but have paradoxical long-term effects when administered during perinatal periods, increasing the risk to develop anxiety and depression. The basis for this developmental effect is not known. Here, we show that during an early postnatal period in mice (P0-P10), Slc6a4/SERT is transiently expressed in a subset of layer 5-6 pyramidal neurons of the prefrontal cortex (PFC). PFC-SERT+ neurons establish glutamatergic synapses with subcortical targets, including the serotonin (5-HT) and GABA neurons of the dorsal raphe nucleus (DRN). PFC-to-DRN circuits develop postnatally, coinciding with the period of PFC Slc6a4/SERT expression. Complete or cortex-specific ablation of SERT increases the number of functional PFC glutamate synapses on both 5-HT and GABA neurons in the DRN. This PFC-to-DRN hyperinnervation is replicated by early-life exposure to the SSRI, fluoxetine (from P2 to P14), that also causes anxiety/depressive-like symptoms. We show that pharmacogenetic manipulation of PFC-SERT+ neuron activity bidirectionally modulates these symptoms, suggesting that PFC hypofunctionality has a causal role in these altered responses to stress. Overall, our data identify specific PFC descending circuits that are targets of antidepressant drugs during development. We demonstrate that developmental expression of SERT in this subset of PFC neurons controls synaptic maturation of PFC-to-DRN circuits, and that remodeling of these circuits in early life modulates behavioral responses to stress in adulthood.
Multifunctional Activities of Green Tea Catechins in Neuroprotection (2005)

Many lines of evidence suggest that oxidative stress resulting in reactive oxygen species (ROS) generation and inflammation play a pivotal role in the age-associated cognitive decline and neuronal loss in neurodegenerative diseases including Alzheimer’s (AD), Parkinson’s (PD) and Huntington’s diseases. One cardinal chemical pathology observed in these disorders is the accumulation of iron at sites where the neurons die. The buildup of an iron gradient in conjunction with ROS (superoxide, hydroxyl radical and nitric oxide) are thought to constitute a major trigger in neuronal toxicity and demise in all these diseases. Thus, promising future treatment of neurodegenerative diseases and aging depends on availability of effective brain permeable, iron-chelatable/radical scavenger neuroprotective drugs that would prevent the progression of neurodegeneration. Tea flavonoids (catechins) have been reported to possess potent iron- chelating, radical-scavenging and anti-inflammatory activities and to protect neuronal death in a wide array of cellular and animal models of neurological diseases. Recent studies have indicated that in addition to the known antioxidant activity of catechins, other mechanisms such as modulation of signal transduction pathways, cell survival/death genes and mitochondrial function, contribute significantly to the induction of cell viability. This review will focus on the multifunctional properties of green tea and its major component (–)-epigallocatechin-3-gallate (EGCG) and their ability to induce neuroprotection and neurorescue in vitro and in vivo. In particular, their transitional metal (iron and copper) chelating property and inhibition of oxidative stress.
Bandwidth efficient communication via a Rayleigh fading channel using RS coded multiphase signaling (1993)

The idea of combining RS (Reed-Solomon) codes with multiphase signaling schemes on fading channels is introduced. The performance of these schemes over a Rayleigh fading channel is evaluated for different decoding strategies, i.e., errors-only, errors-and-erasures, and soft-decision decoding techniques. Both analytical and simulation results show that substantial coding gains are obtained compared to the uncoded reference system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Maternal, Cord, and Neonatal Carnitine Correlations and Lipid Profiles of Various Birthweight Infants (1989)

The carnitine, acylcarnitine, and triglyceride concentrations were determined in the average for gestational age neonates of various birthweights and gestational ages and their corresponding maternal and umbilical cord plasma. Forty-two infants were divided into one of four groups based on birthweight: Group 1, less than 1000 gm; group II, 1001 to 1510 gm; group III, 1511 to 2500 gm; and group IV were term infants who served as the reference group. Results indicated that there was an overall decrease of total carnitine and nonesterified carnitine with advancing gestational age (r = -0.4418, p less than 0.01). Furthermore, there were three distinct phases of plasma carnitine concentrations from 24 weeks to term. The plasma carnitine profile of the neonates less than 1500 gm was strongly correlated (r = 0.73) to their maternal plasma carnitine profile and that of term neonate to their umbilical cord plasma. Acylcarnitine and triglycerides were not significantly correlated.
Utility of 18-Fluorodeoxyglucose positron emission tomography in the prediction of ventricular tachycardia and advanced conduction disease in patients with cardiac sarcoidosis (2018)

The diagnosis and management of cardiac sarcoidosis (CS) along with the recognition of high risk features remains a significant challenge. Failing to identify reliable disease prognosticators often results in fatal ventricular arrhythmia or heart failure.