gebhart/patrepeval huggingface dataset:
Mechanistic-Empirical IRI Model Accounting for Potential Bias (2010)

The roughness prediction models in the International Roughness Index (IRI) currently incorporated into the Mechanistic-Empirical Pavement Design Guide (M-E PDG) have been developed by means of ordinary least squares (OLS). However, some of the variables used in predicting future IRI were previously estimated by means of separate performance models. This could cause bias because of the correlation between the previously estimated distress types and unobserved components on the IRI model. The bias can be corrected by considering additional variables that are correlated with the distress types causing the bias, thus eliminating the correlation to the unobserved terms in the model. Bias in the IRI model can also be generated by unobserved factors not included in the model. If these factors are section-specific, the bias can be removed considering variations in the performance history of different pavement sections. The writers have used updated Long-Term Pavement Performance (LTPP) data consistent with the data set originally used to fit the M-E IRI model for flexible pavements over thick granular bases contained in the M-E PDG. The data were then used in modeling IRI by means of OLS and instrumental variable (IV) regressions analyzing the data as pooled and as a panel data set (by random-effects, fixed-effects, and joint random-effects approach) to check for possible bias in the model. It was found that the current IRI model, as estimated by OLS, exhibits several types of biases attributed to heterogeneity and incorrect assumptions in the modeling process. It was identified that the preferred IRI model was the joint random-effects approach and, therefore, the model parameters were estimated by correcting the omitted-variable bias and simultaneous-equation bias. Estimating the model by accounting for possible bias in the data indicated considerable changes in the effects of different parameters affecting IRI through time, mainly rutting of the pavement structure.
Convenient semihydrogenation of azoarenes to hydrazoarenes using H<sub>2</sub> (2021)

The high atom-economical and eco-benign nature of hydrogenation reactions make them much more superior to conventional reduction and transfer hydrogenation. Herein, a convenient and highly selective hydrogenation reaction of azoarenes using molecular hydrogen to access diverse hydrazoarenes is reported. The present catalytic method is general and operationally simple, and it operates under exceedingly mild conditions (room temperature and 1 atm of hydrogen pressure). The reusability of catalysts used in this method is also successfully demonstrated.
ChemInform Abstract: Synthesis of L,L‐Di‐myo‐inositol‐1,1′‐phosphate: A Novel Inositol Phosphate from Pyrococcus woesei. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A method of task synchronization in a distributed system using FlexRay (2008)

In a distributed system, the synchronization of tasks executed in different nodes is necessary. Therefore, we propose a method of synchronization of tasks in a distributed system using FlexRay. FlexRay is expected to become a dominant protocol in automotive systems. It supports a clock synchronization mechanism. We present two methods for synchronization of tasks using a clock synchronized by FlexRay. One is a synchronization method for the start point of tasks. The other is a synchronization method for specific points in the task. We implement the proposed method as an experiment.
&lt;title&gt;Design and fabrication of optoelectronic multichip module prototypes using MEMS fabrication techniques&lt;/title&gt; (1997)

This paper describes the design, fabrication, and assembly issues of OE-MSMs using MEMS fabrication techniques by characterizing some of the basic building blocks like micromachined silicon mirrors, GaAs MSM photodiodes. Issues of aligning and bonding discrete components discrete components on OE-MCMs are addressed along with the proposed fabrication and packaging strategies. The CMOS compatible TMAH processes are investigated with results comparable to those obtained from KOH processes. After sputtered aluminum layers are applied, the micromachined silicon mirror reflectivities are further improved with some samples showing reflectivities above 95 percent at wavelengths of 1300 nm and 1500 nm. The results from silicon mirror beam profiling and the minor impacts of packaging processes to silicon mirror I/O coupling efficiencies indicate that the mass fabrication of OE-MCM is technically and economically feasible.
Formulation design and pharmaceutical development of a novel controlled release form of azithromycin for single-dose therapy (2009)

Drug release from the microspheres was shown to occur via diffusion through the larger pores formed by dissolution of azithromycin crystals and the smaller interconnected pores formed by dissolution of poloxamer. Several clinical studies have been conducted with the formulation to evaluate its pharmacokinetics and to demonstrate its safety and efficacy. The combined suspension formulation for a 2-g dose of azithromycin provided taste-masking and good tolerability.
Supplementary materials and methods from Induction of Telomere Dysfunction Prolongs Disease Control of Therapy-Resistant Melanoma (2023)

&lt;p&gt;Supplementary materials and methods&lt;/p&gt;
Heat Transfer Enhancement in Forced Convective Boiling in Microchannels by Periodic Electrospun Nanofiber Coatings (2015)

To enhance heat transfer in forced convective boiling the microchannel bottom was amended by a nano-texture - periodic rectangular mats of electrospun polymer nanofibers. The fibers were ~ 300-500 nm in diameter and the mat thicknesses were about 6-15 μm. The test fluid was FC-72 and the flow in microchannels contained trains of Taylor bubbles. The role of the nanofibers was to retain the warm microchannel bottom wet, to prevent dry-out and thus to enhance the heat removal rate. In the present experiments the time-average heat flux and heat transfer coefficient at the nanofiber-coated domains were found to be 1.5-2 times higher than those at the uncoated ones. Accordingly, a significant decrease (by 5-8 K) in the superheat was observed at the same Re of 387 and power supply of 36.1 kW/m2. At a higher Re of 432 and lower power supply of 28.1 kW/m2 similar trends in the heat removal rate and surface superheat were found. The significant enhancement of the heat transfer results from the fact that nanofiber mats facilitate wetting of surface under passing Taylor bubbles, thus delaying formation of vapor flow at the channel bottom. The interstices of the nanofiber mat act as the nucleation sites facilitating formation of tiny bubbles, which eventually results in a higher heat removal rate from the surface at a reduced superheat.
In VitroAnalysis of Hrd1p-mediated Retrotranslocation of Its Multispanning Membrane Substrate (2009)

Endoplasmic reticulum (ER)-associated degradation (ERAD) is responsible for the ubiquitin-mediated destruction of both misfolded and normal ER-resident proteins. ERAD substrates must be moved from the ER to the cytoplasm for ubiquitination and proteasomal destruction by a process called retrotranslocation. Many aspects of retrotranslocation are poorly understood, including its generality, the cellular components required, the energetics,andthemechanismoftransferthroughtheERmembrane.Toaddressthesequestions,wehavedevelopedaninvitro assay, using the 8-transmembrane span ER-resident Hmg2p isozymeofHMG-CoAreductasefusedtoGFP,whichundergoes regulated ERAD mediated by the Hrd1p ubiquitin ligase. We have now directly demonstratedin vitroretrotranslocation of full-length, ubiquitinated Hmg2p-GFP to the aqueous phase. Hrd1p was rate-limiting for Hmg2p-GFP retrotranslocation, which required ATP, the AAA-ATPase Cdc48p, anditsreceptor Ubx2p. In addition, the adaptors Dsk2p and Rad23p, normally implicated in later parts of the pathway, were required. Hmg2pGFPretrotranslocationdidnotdependonanyoftheproposedER channel candidates. To examine the role of the Hrd1p transmembrane domain as a retrotranslocon, we devised a self-ubiquitinating polytopic substrate (Hmg1-Hrd1p) that undergoes ERAD in the absence of Hrd1p.In vitroretrotranslocation of full-length Hmg1-Hrd1p occurred in the absence of the Hrd1p transmembrane domain, indicating that it did not serve a required channel function.Thesestudiesdirectlydemonstratepolytopicmembrane proteinretrotranslocationduringERADanddelineateavenuesfor mechanisticunderstandingofthisgeneralprocess.
From cellulosomes to cellulosomics (2008)

Cellulosomes are intricate multienzyme systems produced by several cellulolytic bacteria, the first example of which was discovered in the anaerobic thermophilic bacterium, Clostridium thermocellum. Cellulosomes are designed for efficient degradation of plant cell wall polysaccharides, notably cellulose--the most abundant renewable polymer on earth. The component parts of the multicomponent complex are integrated by virtue of a unique family of integrating modules, the cohesins and the dockerins, whose distribution and specificity dictate the overall cellulosome architecture. A full generation of research has elapsed since the original publications that documented the cellulosome concept. In this review, we provide a personal account on the discovery process, while describing how divergent cellulosome systems were identified and investigated, culminating in the collaboration of several labs worldwide to tackle together the challenging field of cellulosome genomics and metagenomics.
The FIGO Ovulatory Disorders Classification System (2022)

Ovulatory disorders are common causes of amenorrhea, abnormal uterine bleeding and infertility and are frequent manifestations of polycystic ovary syndrome (PCOS). There are many potential causes and contributors to ovulatory dysfunction that challenge clinicians, trainees, educators, and those who perform basic, translational, clinical and epidemiological research. Similarly, therapeutic approaches to ovulatory dysfunction potentially involve a spectrum of lifestyle, psychological, medical and procedural interventions. Collaborative research, effective education and consistent clinical care remain challenged by the absence of a consensus comprehensive system for classification of these disorders. The existing and complex system, attributed to the World Health Organization (WHO), was developed more than three decades ago and did not consider more than 30 years of research into these disorders in addition to technical advances in imaging and endocrinology. This article describes the development of a new classification of ovulatory disorders performed under the aegis of the International Federation of Gynecology and Obstetrics (FIGO) and conducted using a rigorously applied Delphi process. The stakeholder organizations and individuals who participated in this process comprised specialty journals, experts at large, national, specialty obstetrical and gynecological societies, and informed lay representatives. After two face-to-face meetings and five Delphi rounds, the result is a three-level multi-tiered system. The system is applied after a preliminary assessment identifies the presence of an ovulatory disorder. The primary level of the system is based on an anatomic model (Hypothalamus, Pituitary, Ovary) that is completed with a separate category for PCOS. This core component of the system is easily remembered using the acronym HyPO-P. Each anatomic category is stratified in the second layer of the system to provide granularity for investigators, clinicians and trainees using the 'GAIN-FIT-PIE' mnemonic (Genetic, Autoimmune, Iatrogenic, Neoplasm; Functional, Infectious and Inflammatory, Trauma and Vascular; Physiological, Idiopathic, Endocrine). The tertiary level allows for specific diagnostic entities. It is anticipated that, if widely adopted, this system will facilitate education, clinical care and the design and interpretation of research in a fashion that better informs progress in this field. Integral to the deployment of this system is a periodic process of reevaluation and appropriate revision, reflecting an improved understanding of this collection of disorders.
Complex Presentation of Hao-Fountain Syndrome Solved by Exome Sequencing Highlighting Co-Occurring Genomic Variants (2022)

The co-occurring variants in <i>USP7</i> and <i>CFTR</i> variants explained the multisystem disorder of the patient. The comprehensive dissection of the phenotype and early diagnosis of autosomal dominant polycystic kidney disease allowed us to manage the <i>CFTR</i>-related disorder symptoms and monitor renal function and other complications associated with <i>PKD2</i> haploinsufficiency, addressing proper care and surveillance.
MARVEL: A wireless Miniature Anchored Robotic Videoscope for Expedited Laparoscopy (2012)

This paper describes the design and implementation of a Miniature Anchored Robotic Videoscope for Expedited Laparoscopy (MARVEL) and Camera Module (CM) that features wireless communications and control. The CM decreases the surgical-tool bottleneck experienced by surgeons in state-of-the art Laparoscopic Endoscopic Single-Site (LESS) procedures for minimally invasive abdominal surgery. The system includes: (1) a near-zero latency video wireless communications link, (2) a pan/tilt camera platform, actuated by two motors that provides surgeons a full hemisphere field of view inside the abdominal cavity, (3) a small wireless camera, (4) a wireless illumination control system, and (5) a wireless human-machine interface (HMI) to control the CM. An in-vivo experiment on a porcine subject was carried out to test the performance of the system. The robotic design is a Research Platform for a broad range of experiments in a range of domains for faculty and students in the Colleges of Engineering and Medicine and at Tampa General Hospital. This research is the first step in developing semi-autonomous wirelessly controlled and networked laparoscopic devices to enable a paradigm shift in minimally invasive surgery and other domains such as Wireless Body Area Networks.
Correlation and Morphology of Dopant Decomposition in Mn and Co Codoped Ge Epitaxial Films (2011)

Atom probe tomography (APT) was used to quantify inhomogeneities in the distribution of Mn and Co in doped epitaxial Ge thin films for which X-ray diffraction (XRD) studies indicate single phase material. The segregation of dopants into Co and Mn-rich regions with characteristic sizes was evident upon visual inspection of the APT reconstruction and a frequency distribution analysis of the concentration of Co, Mn, and Ge atoms verified that the composition fluctuations exceeded those of a random alloy. Isoconcentration surfaces were generated to establish the connectedness of regions enriched in Mn that have been proposed to enhance the Curie temperature in dilute magnetic semiconductors. The analysis demonstrates important contributions that APT can make to the understanding of magnetism in these materials.
Movers, shakers, and storers of charge: The legacy of ferroelectricians L. Eric Cross and Robert E. Newnham (2017)

Abstract The last 100 years has seen the burgeoning of the field of ferroelectrics from a scientific curiosity to the basis of major industries in capacitors, piezoelectrics, and electro‐optics. This paper will discuss the history of the field, with an emphasis on the contributions made by Professors Robert E. Newnham and L. Eric Cross of the Pennsylvania State University. Their scientific contributions encompassed many key areas in ferroelectrics, including phenomenology, structure determination, relaxor ferroelectrics, composite piezoelectrics, structure‐property relations, and flexoelectricity. Scientific advances were often motivated by and closely coupled with application needs. Finally, their impact on global academic communities is discussed.
Mapping the functional domains of TCblR/ <i>CD320</i> , the receptor for cellular uptake of transcobalamin‐bound cobalamin (2013)

The membrane receptor TCblR/CD320 binds transcobalamin (TC) saturated with vitamin B12 [cobalamin (Cbl)] and mediates cellular uptake of the vitamin. The specificity of TC for Cbl and of the receptor for TC-Cbl ensures efficient uptake of Cbl into cells. The high-affinity interaction of TCblR with TC-Cbl (Ka=10 nM(-1)) was investigated using deletions and mutations of amino acid sequences in TCblR. Only the extracellular region (aa 32-229) is needed for TC-Cbl binding, but the N-glycosylation sites (N126, N195, and N213) are of no importance for this function. Deleting the cysteine-rich region (aa 95-141) that separates the two low-density lipoprotein receptor type A (LDLR-A) domains does not affect TC-Cbl binding (Ka = 19-24 nM(-1)). The two LDLR-A domains (aa 54-89 and 132-167) with the negatively charged acidic residues involved in Ca(2+) binding are critical determinants of ligand binding. The cytoplasmic tail is apparently crucial for internalization of the ligand. Within this region, the RPLGLL motif and the PDZ binding motifs (QERL/KESL) appear to be involved in initiating and completing the process of ligand internalization. Mutations and deletions of these regions involved in binding and internalization of TC-Cbl are likely to produce the biochemical and clinical phenotype of Cbl deficiency.
HDAC inhibitors conquer polycomb proteins (2010)

Parkinson disease is caused by the progressive loss of dopamine innervation to the basal ganglia and is commonly treated with the dopamine precursor, L-DOPA. Prolonged administration of L-DOPA results in the development of severe motor complications or dyskinesia, which seriously hamper its clinical use. Recent evidence indicates that L-DOPA-induced dyskinesia (LID) is associated with persistent activation of the mammalian target of rapamycin complex 1 (mTORC1) in the medium spiny neurons (MSNs) of the striatum, the main component of the basal ganglia. This phenomenon is secondary to the development of a strong sensitization at the level of dopamine D1 receptors, which are abundantly expressed in a subset of MSNs. Such sensitization confers to dopaminergic drugs (including L-DOPA) the ability to activate the extracellular signal-regulated protein kinases 1/2, which, in turn promote mTORC1 signaling. Using a mouse model of LID, we recently showed that administration of the allosteric mTORC1 inhibitor, rapamycin, reduces dyskinesia. This finding is discussed with respect to underlying mechanisms and potential significance for the development of future therapeutic interventions.
A low cost and hybrid technology for integrating silicon sensors or actuators in polymer microfluidic systems (2007)

This paper describes a new technology permitting a hybrid integration of silicon chips in polymer (PDMS and SU8) microfluidic structures. This two-step technology starts with transferring the silicon device onto a rigid substrate (typically PCB) and planarizing it, and then it proceeds with stacking of the polymer-made fluidic network onto the device. The technology is low cost, based on screen printing and lamination, can be applied to treat large surface areas, and is compatible with standard photolithography and vacuum based approaches. We show, as an example, the integration of a thermal sensor inside channels made of PDMS or SU8. The developed structures had no fluid leaks at the Si/polymer interfaces and the electrical circuit was perfectly tightproof.
Contrast improvement in scattered light confocal imaging of skin birefringent structures by depolarization detection (2011)

Here we describe a method for enhancing the contrast in imaging skin birefringent structures. The method relies on polarization-dependent optical properties and is implemented using cross polarized confocal microscopy. The experimental data obtained using ex-vivo and in-vivo measurements on human scalp hairs and human skin demonstrate a significant dependence of the change in polarization of light that interacted with the birefringent hair on the orientation of the incident polarization. The polarization dependent contrast, defined as the ratio of intensity measured for different orientations of the incident polarization when observed using cross polarized confocal microscopy furthermore depends on the hair type/degree of pigmentation and on the focusing depth inside the hair. No such dependence was observed for the upper skin layers, including the stratum corneum and epidermis. We propose a new method for enhancing the contrast between the skin and the birefringent hair by the use of cross polarized confocal microscopy combined with the variation of the polarization of the incoming light. Potential applications of this method include imaging of hairs for assessing the efficacy of hair removal methods and measurement of skin birefringence. The underestimation of the birefringence content resulting from the orientation related effects associated with the use of linearly polarized light for imaging tissues containing wavy birefringent structures could be minimized by this method.
PAGER: constructing PAGs and new PAG–PAG relationships for network biology (2023)

Pathway and Annotated-list Gene-signature Electronic Repository (PAGER) is an online systems biology tool for constructing and visualizing gene and PAG networks from multiple PAG genesets. PAG stands for Pathway, Annotated-list and Gene-signature. A PAG geneset represents a set of genes that share a common feature, whether they belong within the same pathway, share common biological processes, are co-differentially expressed under a particular condition of an experiment or clinical sample, or share a common downstream target or function. <strong>Available at:</strong> http://discovery.informatics.uab.edu/PAGER <strong>Acknowledgements:</strong> Zongliang Yue, Qi Zheng, Michael T Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y Chen, PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D668–D676,https://doi.org/10.1093/nar/gkx1040 <strong>File description</strong> The GMT file format is a tab delimited file format that describes gene sets. In the GMT format, each row represents a PAG. The first column is PAG identifier, the second column is PAG link and the third and left columns are PAG genes.