gebhart/patrepeval huggingface dataset:
The leader region of Laminin B1 mRNA confers cap-independent translation (2007)

Translation initiation of eukaryotic mRNAs generally occurs by cap-dependent ribosome scanning. However, certain mRNAs contain internal ribosome entry sites (IRES) allowing cap-independent translation. Several of these IRES-competent transcripts and their corresponding proteins are involved in tumourigenesis. This study focused on IRES-driven translation control during the epithelial to mesenchymal transition (EMT) of hepatocytes that reflects crucial aspects of carcinoma progression. Expression profiling of EMT revealed Laminin B1 (LamB1) to be translationally upregulated. The 5'-untranslated region (UTR) of LamB1 was potent to direct IRES-dependent mRNA utilization of a bicistronic reporter construct. Stringent assays for cryptic promoter and splice sites showed no aberrantly expressed transcripts, suggesting that the reporter activity provided by the leader region of LamB1 mRNA exclusively depends on IRES. In accordance, LamB1 expression increased upon negative interference with cap-dependent translation by expression of human rhinovirus 2A protease or heat shock of cells. Finally, the enhanced expression of LamB1 during EMT correlated with an elevated IRES activity. Together, these data provide first evidence that the 5'-UTR of LamB1 contains a bona fide IRES that directs translational upregulation of LamB1 during stress conditions and neoplastic progression of hepatocytes.
Parallelizable algorithms for the selection of grouped variables (2011)

Well-appreciated in statistics for its ability to select relevant grouped features (factors) in linear regression models, the group-Lasso estimator has been fruitfully applied to diverse signal processing problems including RF spectrum cartography and robust layered sensing. These applications motivate the distributed group-Lasso algorithm developed in this paper, that can be run by a network of wireless sensors, or, by multiple processors to balance the load of a single computational unit. After reformulating the group-Lasso cost into a separable form, it is iteratively minimized using the method of multipliers to obtain parallel per agent and per factor estimate updates given by vector soft-thresholding operations. Through affordable inter-agent communication of sparse messages, the local estimates provably consent to the global group-Lasso solution. Specializing to a single agent network, or, to univariate factors, efficient (distributed) Lasso solvers are rediscovered as a byproduct.
Bit-interleaved low density spread (BI-LDS) transmission (2014)

Achieving higher aggregate data rates for many simultaneous users is considered as a fundamental challenge for the next generation of wireless systems. With low-density spreading (LDS), one could transmit information by overloading, i.e., using more spreading sequences than chips with reasonable implementation complexity. In this paper, we propose an improvement to the conventional LDS technique that consists in introducing a bit interleaver in the transmission scheme. Its role is to render the error bursts that appear at the output of the LDS detector into correctable patterns for the channel decoder. Numerical evaluations of the spectral efficiency show SNR improvements of more than 2dB when using convolutional codes in BI-LDS schemes. Slight improvements are also observed when turbo codes are employed.
Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment (2015)

Cognitive deficits and reduced educational achievement are common in psychiatric illness; understanding the genetic basis of cognitive and educational deficits may be informative about the etiology of psychiatric disorders. A recent, large genome-wide association study (GWAS) reported a genome-wide significant locus for years of education, which subsequently demonstrated association to general cognitive ability ("g") in overlapping cohorts. The current study was designed to test whether GWAS hits for educational attainment are involved in general cognitive ability in an independent, large-scale collection of cohorts. Using cohorts in the Cognitive Genomics Consortium (COGENT; up to 20,495 healthy individuals), we examined the relationship between g and variants associated with educational attainment. We next conducted meta-analyses with 24,189 individuals with neurocognitive data from the educational attainment studies, and then with 53,188 largely independent individuals from a recent GWAS of cognition. A SNP (rs1906252) located at chromosome 6q16.1, previously associated with years of schooling, was significantly associated with g (P = 1.47 × 10(-4) ) in COGENT. The first joint analysis of 43,381 non-overlapping individuals for this a priori-designated locus was strongly significant (P = 4.94 × 10(-7) ), and the second joint analysis of 68,159 non-overlapping individuals was even more robust (P = 1.65 × 10(-9) ). These results provide independent replication, in a large-scale dataset, of a genetic locus associated with cognitive function and education. As sample sizes grow, cognitive GWAS will identify increasing numbers of associated loci, as has been accomplished in other polygenic quantitative traits, which may be relevant to psychiatric illness.
Hall and Seebeck measurement of ap-nlayer stack: Determining InN bulk hole transport properties in the presence of a strong surface electron accumulation layer (2012)

Measuring $p$-type transport properties by the Hall method in the presence of a parallel $n$-type carrier system with higher mobility is challenging as the measurement often indicates an apparent $n$-type conductivity. For example, the presence of the strong surface electron accumulation layer in $p$-type doped InN has thwarted even the qualitative assignment of $p$-type conductivity by Hall measurements. We present a method to determine the hole transport properties---resistivity, concentration, activation energy, and mobility---by combined multilayer modeling and Hall measurements of samples with different thicknesses of the $p$-type layer in parallel to a thickness-independent $n$-type carrier system. This method is further extended to determine the hole Seebeck coefficient, and can be generally used to determine the properties of one volume carrier system in any mixed ($p$ and $n$) conductivity stack. By applying this method to Mg-doped InN we unambiguously prove $p$-type conductivity by Hall measurements, and determine the hole transport properties, which reveal an unexpectedly high hole Seebeck coefficient at the present hole concentration.
How LinkedIn Economic Graph Bonds Information and Product: Applications in LinkedIn Salary (2018)

The LinkedIn Salary product was launched in late 2016 with the goal of providing insights on compensation distribution to job seekers, so that they can make more informed decisions when discovering and assessing career opportunities. The compensation insights are provided based on data collected from LinkedIn members and aggregated in a privacy-preserving manner. Given the simultaneous desire for computing robust, reliable insights and for having insights to satisfy as many job seekers as possible, a key challenge is to reliably infer the insights at the company level when there is limited or no data at all. We propose a two-step framework that utilizes a novel, semantic representation of companies (Company2vec) and a Bayesian statistical model to address this problem. Our approach makes use of the rich information present in the LinkedIn Economic Graph, and in particular, uses the intuition that two companies are likely to be similar if employees are very likely to transition from one company to the other and vice versa. We compute embeddings for companies by analyzing the LinkedIn members' company transition data using machine learning algorithms, then compute pairwise similarities between companies based on these embeddings, and finally incorporate company similarities in the form of peer company groups as part of the proposed Bayesian statistical model to predict insights at the company level. We perform extensive validation using several different evaluation techniques, and show that we can significantly increase the coverage of insights while, in fact, even improving the quality of the obtained insights. For example, we were able to compute salary insights for 35 times as many title-region-company combinations in the U.S. as compared to previous work, corresponding to 4.9 times as many monthly active users. Finally, we highlight the lessons learned from deployment of our system.
All-dielectric superchiral-field-enhanced Raman optical activity (2021)

<strong>Raman optical activity (ROA) is effective for studying the conformational structure and behavior of chiral molecules in aqueous solutions and is advantageous over X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy in sample preparation and cost performance. However, ROA signals are inherently min</strong><strong>u</strong><strong>scule; 3–5 orders of magnitude weaker than spontaneous Raman scattering due to the weak chiral light-matter interaction. Localized surface plasmon resonance (LSPR) on metallic nanoparticles has been employed to enhance ROA signals, but suffers from detrimental spectral artifacts due to its photothermal heat generation and inability to efficiently transfer and enhance optical chirality from the far field to the near field. Here we demonstrate all-dielectric superchiral-field-enhanced ROA by devising a silicon nanodisk array and exploiting </strong><strong>its hybrid</strong> <strong>mode<sup> </sup>to overcome these limitations. Specifically, we use it with pairs of chemical and biological enantiomers to show &gt;100x enhanced chiral light-molecule interaction with negligible artifacts for ROA measurement</strong><strong>s</strong><strong>. </strong>
Preferential deadenylation of Hsp70 mRNA plays a key role in regulating Hsp70 expression in Drosophila melanogaster. (1994)

Following a standard heat shock, approximately 40% of Hsp70 transcripts in Drosophila melanogaster lack a poly(A) tail. Since heat shock disrupts other aspects of RNA processing, this observation suggested that heat might disrupt polyadenylation as well. We find, however, that as the temperature is increased a larger fraction of Hsp70 RNA is polyadenylated. Poly(A)-deficient Hsp70 RNAs arise not from a failure in polyadenylation but from the rapid and selective removal of poly(A) from previously adenylated transcripts. Poly(A) removal is highly regulated: poly(A) is (i) removed much more rapidly from Hsp70 RNAs than from Hsp23 RNAs, (ii) removed more rapidly after mild heat shocks than after severe heat shocks, and (iii) removed more rapidly after a severe heat shock if cells have first been conditioned by a mild heat treatment. Poly(A) seems to be removed by simple deadenylation rather than by endonucleolytic cleavage 5' of the adenylation site. During recovery from heat shock, deadenylation is rapidly followed by degradation. In cells maintained at high temperatures, however, the two processes are uncoupled and Hsp70 RNAs are deadenylated without being degraded. These deadenylated mRNAs are translated with low efficiency. Deadenylation therefore allows Hsp70 synthesis to be repressed even when degradation of the mRNA is blocked. Poly(A) tail shortening appears to play a key role in regulating Hsp70 expression.
P-Selectin–Mediated Platelet-Neutrophil Aggregate Formation Activates Neutrophils in Mouse and Human Sickle Cell Disease (2010)

Our findings suggest that platelet binding activates neutrophils and contributes to a chronic inflammatory state and pulmonary dysfunction in SCD. The inhibition of platelet activation may be useful to decrease tissue injury in SCD, particularly during the early stages of vaso-occlusive crises.
Age‐Dependent Predictive Value of Endothelial Dysfunction for Arrhythmia Recurrence Following Pulmonary Vein Isolation (2016)

The risk associated with endothelial dysfunction for arrhythmia recurrence following catheter ablation was age dependent and was higher in younger participants.
Triplet Harvesting in Hybrid White Organic Light‐Emitting Diodes (2009)

Abstract White organic light‐emitting diodes (OLEDs) are highly efficient large‐area light sources that may play an important role in solving the global energy crisis, while also opening novel design possibilities in general lighting applications. Usually, highly efficient white OLEDs are designed by combining three phosphorescent emitters for the colors blue, green, and red. However, this procedure is not ideal as it is difficult to find sufficiently stable blue phosphorescent emitters. Here, a novel approach to meet the demanding power efficiency and device stability requirements is discussed: a triplet harvesting concept for hybrid white OLED, which combines a blue fluorophor with red and green phosphors and is capable of reaching an internal quantum efficiency of 100% if a suitable blue emitter with high‐lying triplet transition is used is introduced. Additionally, this concept paves the way towards an extremely simple white OLED design, using only a single emitter layer.
Leveraging Circuit Edit for Low-Volume Trusted Nanometer Fabrication (2017)

This chapter reviews a recently proposed technique that leverages circuit-edit technology to support design obfuscation and trusted fabrication. The shortcoming of such an approach is that it is limited to low-volume production since circuit edit can be performed only on a chip-by-chip basis. The proposed circuit edit-based technique could compete with such approaches for ensuring trusted fabrication. For logic encryption and circuit edit-based obfuscation, further work is required to look into distribution of key gates/gate-level modifications between different IP cores. One side-effect of such contamination is an increased resistivity of interconnect/vias that have been created by circuit edit. The chapter discusses gate-level changes that can be implemented by the design house/designer on such controller units for circuit edit–enabled obfuscation. Split manufacturing enables the splitting of the fabrication process between an untrusted and a trusted foundry. Although circuit edit-based obfuscation makes trusted low-volume fabrication possible, there is a potential concern regarding the performance and reliability of circuit-edited chips.
The Use of a Continuous Glucose Monitoring System in Hypoglycemic Disorders (2004)

CGMS is a useful adjunct in the diagnosis and evaluation of hypoglycemia, and for documentation of euglycemia in these patients following therapy.
Inactivation of Chibby affects function of motile airway cilia (2020)

Chibby (Cby) is a conserved component of the Wnt–β-catenin pathway. Cby physically interacts with β-catenin to repress its activation of transcription. To elucidate the function of Cby in vertebrates, we generated Cby−/− mice and found that after 2–3 d of weight loss, the majority of mice die before or around weaning. All Cby−/− mice develop rhinitis and sinusitis. When challenged with Pseudomonas aeruginosa isolates, Cby−/− mice are unable to clear the bacteria from the nasal cavity. Notably, Cby−/− mice exhibit a complete absence of mucociliary transport caused by a marked paucity of motile cilia in the nasal epithelium. Moreover, ultrastructural experiments reveal impaired basal body docking to the apical surface of multiciliated cells. In support of these phenotypes, endogenous Cby protein is localized at the base of cilia. As the phenotypes of Cby−/− mice bear striking similarities to primary ciliary dyskinesia, Cby−/− mice may prove to be a useful model for this condition.
Optimization of antireflection structures of polymer based on nanoimprinting using anodic porous alumina (2008)

The optimization of antireflection (AR) structures of polymer composed of an ordered array of tapered pillars was studied. An anodic porous alumina mold with precisely controlled tapered holes was prepared and used for photoimprinting of the polymer. The reflectance of the obtained AR polymer structures with conical pillars was evaluated through the measurement of transmittance. Among the AR structures with pillars with various slopes, those with a gradually changing slope exhibited the lowest reflectance. The fabrication process will be effective for the formation of an AR surface with minimized reflectance over a large sample area.
Regulation of jun -B Messenger RNA and AP-1 Activity by Light and a Circadian Clock (1992)

The suprachiasmatic nuclei (SCN) of the hypothalamus comprise the primary pacemaker responsible for generation of circadian rhythms in mammals. Light stimuli that synchronize this circadian clock induce expression of the c-fos gene in rodent SCN, which suggests a possible role for Fos in circadian entrainment. Appropriate light stimuli also induce the expression of jun-B messenger RNA in the SCN of golden hamsters but only slightly elevate c-jun messenger RNA levels. In addition, light increases the amount of a protein complex in the SCN that binds specifically to sites on DNA known to mediate regulation by the AP-1 transcription factor. The photic regulation of both jun-B messenger RNA expression and AP-1 binding activity is dependent on circadian phase: only light stimuli that shift behavioral rhythms induce jun-B and AP-1 expression. Thus, light and the circadian pacemaker interact to regulate a specific set of immediate-early genes in the SCN that may participate in entrainment of the circadian clock.
Personalized psychiatry: a realistic goal (2004)

It is becoming increasingly evident that the implementation of true personalized medicine will not come as rapidly and smoothly as initially hoped. In the aftermath of the drafting of the human genome in 2001, the popular and scientific media featured numerous commentaries heralding the approaching arrival of personalized medicine to the clinic, and describing its huge benefits for patients. Media coverage predicted a drastic transformation for the practice of medicine, second to the revolution brought about by the discovery of vaccines and antibiotics. From the perspective of another 3 years, during which substantial new insights were made into the enormous complexity of human genome variation, it seems that true personalized medicine may still be decades away for many aspects of medical treatment. Nonetheless, the prospects for implementation of at least certain elements of personalized medicine for one key discipline, psychiatry, might be relatively close and more realistic. With the correct focus, realization of some benefits of genetic patient profiling for psychiatric pharmacotherapy might be near, and in due course, lead the way for true personalized psychiatry.
Frequency-Specific Optogenetic Deep Brain Stimulation of Subthalamic Nucleus Improves Parkinsonian Motor Behaviors (2020)

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an effective therapy for the motor symptoms of Parkinson's disease (PD). However, the neural elements mediating symptom relief are unclear. A previous study concluded that direct optogenetic activation of STN neurons was neither necessary nor sufficient for relief of parkinsonian symptoms. However, the kinetics of the channelrhodopsin-2 (ChR2) used for cell-specific activation are too slow to follow the high rates required for effective DBS, and thus the contribution of activation of STN neurons to the therapeutic effects of DBS remains unclear. We quantified the behavioral and neuronal effects of optogenetic STN DBS in female rats following unilateral 6-hydroxydopamine (6-OHDA) lesion using an ultrafast opsin (Chronos). Optogenetic STN DBS at 130 pulses per second (pps) reduced pathologic circling and ameliorated deficits in forelimb stepping similarly to electrical DBS, while optogenetic STN DBS with ChR2 did not produce behavioral effects. As with electrical DBS, optogenetic STN DBS exhibited a strong dependence on stimulation rate; high rates produced symptom relief while low rates were ineffective. High-rate optogenetic DBS generated both increases and decreases in firing rates of single neurons in STN, globus pallidus externa (GPe), and substantia nigra pars reticular (SNr), and disrupted β band oscillatory activity in STN and SNr. High-rate optogenetic STN DBS can indeed ameliorate parkinsonian motor symptoms through reduction of abnormal oscillatory activity in the STN-associated neural circuit, and these results highlight that the kinetic properties of opsins have a strong influence on the effects of optogenetic stimulation.<b>SIGNIFICANCE STATEMENT</b> Whether STN local cells contribute to the therapeutic effects of subthalamic nucleus (STN) deep brain stimulation (DBS) in Parkinson's disease (PD) remains unclear. We re-examined the role of STN local cells in mediating the symptom-relieving effects of STN DBS using cell type-specific optogenetic stimulation with a much faster opsin, Chronos. Direct optogenetic stimulation of STN neurons was effective in treating the symptoms of parkinsonism in the 6-hydroxydopamine (6-OHDA) lesion rat. These results highlight that the kinetic properties of opsins can have a strong influence on the effects of optogenetic activation/inhibition and must be considered when employing optogenetic to study high-rate neural stimulation.
Power grid analysis benchmarks (2008)

Benchmarks are an immensely useful tool in performing research since they allow for rapid and clear comparison between different approaches to solving CAD problems. Recent experience from the placement [1] and routing [2] areas suggests that the ready availability of realistic industrial-size benchmarks can energize research in a given area, and can even lead to significant breakthroughs. To this end, we are making a number of power grid analysis benchmarks available for the public. These are all drawn from real designs, and vary over a reasonable range of size and difficulty thereby making studies of algorithm complexity possible. This paper documents the format for the various benchmarks, and give details for their access.
Uromodulin (Tamm-Horsfall Glycoprotein): a Renal Ligand for Lymphokines (1987)

The protein portion of the immunosuppressive glycoprotein uromodulin is identical to the Tamm-Horsfall urinary glycoprotein and is synthesized in the kidney. Evidence that the glycoproteins are the same is based on amino acid sequence identity, immunologic cross-reactivity, and tissue localization to the thick ascending limb of Henle's loop. Nucleic acid sequencing of clones for uromodulin isolated from a complementary DNA bank from human kidney predicts a protein 639 amino acids in length, including a 24--amino acid leader sequence and a cysteine-rich mature protein with eight potential glycosylation sites. Uromodulin and preparations of Tamm-Horsfall glycoprotein bind to recombinant murine interleukin-1 (rIL-1) and human rIL-1 alpha, rIL-1 beta, and recombinant tumor necrosis factor (rTNF). Uromodulin isolated from urine of pregnant women by lectin adherence is more immunosuppressive than material isolated by the original salt-precipitation protocol of Tamm and Horsfall. Immunohistologic studies demonstrate that rIL-1 and rTNF bind to the same area of the human kidney that binds to antiserum specific for uromodulin. Thus, uromodulin (Tamm-Horsfall glycoprotein) may function as a unique renal regulatory glycoprotein that specifically binds to and regulates the circulating activity of a number of potent cytokines, including IL-1 and TNF.
Channel Measurement/Modeling for Airport Surface Communications: Mobile and Fixed Platform Results (2007)

We provide examples of measurement and modeling results for wireless channel characteristics around airport surface areas. This is done for three settings: two mobile settings and one non-mobile setting, in the 5 GHz Microwave Landing System extension band. New findings, useful for communication system design in this environment, are reported.