gebhart/patrepeval huggingface dataset:
Nitrogen process in stormwater bioretention: effect of the antecedent dry days on the relative abundance of nitrogen functional genes (2022)

In this study, we evaluated the relative abundance of nitrogen functional genes (amoA, nirK and nirS) involved in ammonia oxidation and denitrification bacteria in laboratory-scale bioretention columns in response to environmental factors (e.g., moisture content, pH, soil organic matter, soil nitrogen) under different antecedent dry days (ADDs). We observed a decrease tendency of the relative abundance of ammonia-oxidizing bacteria at first and then increased when increasing ADDs from 1 to 22 day, while the relative abundance of denitrifying bacteria showed a downward trend. The abundance of bacteria gene amoA was positively associated with soil ammonia nitrogen concentration (r<sup>2</sup> = 0.389, p < 0.05) and soil organic matter concentration (r<sup>2</sup> = 0.334, p < 0.05), while the abundance of bacteria gene nirS was positively correlated with soil ammonia nitrogen (r<sup>2</sup> = 0.730, p < 0.01), soil organic matter (r<sup>2</sup> = 0.901, p < 0.01) and soil total nitrogen (r<sup>2</sup> = 0.779, p < 0.01). Furthermore, gene counts for bacteria gene nirS were correlated negatively with plant root length (r<sup>2</sup> = 0.364, p < 0.05) and plant biomass (r<sup>2</sup> = 0.381, p < 0.05). Taken together, these results suggest that both nitrification and denitrification can occur in bioretention systems, which can be affected by environmental factors.
Statistical framework for validation without ground truth of choroidal thickness changes detection (2019)

Monitoring subtle choroidal thickness changes in the human eye delivers insight into the pathogenesis of various ocular diseases such as myopia and helps planning their treatment. However, a thorough evaluation of detection-performance is challenging as a ground truth for comparison is not available. Alternatively, an artificial ground truth can be generated by averaging the manual expert segmentations. This makes the ground truth very sensitive to ambiguities due to different interpretations by the experts. In order to circumvent this limitation, we present a novel validation approach that operates independently from a ground truth and is uniquely based on the common agreement between algorithm and experts. Utilizing an appropriate index, we compare the joint agreement of several raters with the algorithm and validate it against manual expert segmentation. To illustrate this, we conduct an observational study and evaluate the results obtained using our previously published registration-based method. In addition, we present an adapted state-of-the-art evaluation method, where a paired t-test is carried out after leaving out the results of one expert at the time. Automated and manual detection were performed on a dataset of 90 OCT 3D-volume stack pairs of healthy subjects between 8 and 18 years of age from Asian urban regions with a high prevalence of myopia.
ON-LINE ACTION RECOGNITION FROM SPARSE FEATURE FLOW (2012)

The fast and robust recognition of human actions is an important aspect for many video-based applications in the field of human computer interaction and surveillance. Although current recognition algorithms provide more and more advanced results, their usability for on-line applications is still limited. To bridge this gap a online video-based action recognition system is presented that combines histograms of sparse feature point flow with an HMM-based action recognition. The usage of feature point motion is computational more efficient than the more common histograms of optical flow (HoF) by reaching a similar recognition accuracy. For recognition we use low-level action units that are modeled by Hidden-Markov-Models (HMM). They are assembled by a context free grammar to recognize complex activities. The concatenation of small action units to higher level tasks allows the robust recognition of action sequences as well as a continuous on-line evaluation of the ongoing activity. The average runtime is around 34 ms for processing one frame and around 20 ms for calculating one hypothesis for the current action. Assuming that one hypothesis per second is needed, the system can provide a mean capacity of 25 fps. The systems accuracy is compared with state of the art recognition results on a common benchmark dataset as well as with a marker-based recognition system, showing similar results for the given evaluation scenario. The presented approach can be seen as a step towards the on-line evaluation and recognition of human motion directly from video data.
Validation of a STATCOM Transient Stability Model through Small-Disturbance Stability Studies (2007)

Synchronous STATic COMpensator (STATCOM) controllers are being more prevalently used to address some voltage and angle stability and control problems, especially in distribution systems with the advent of microgrids. Thus, this paper discusses the validity of a typical transient stability (TS) model of a STATCOM widely used in small-disturbance stability studies of large, interconnected power grids as well as microgrids. EMTDC/PSCAD-based time domain simulations for both TS and detailed models, with a standard control and a supplementary control, are used as the basis for comparison and validation. A system identification technique, i.e. the Prony method, is applied to the time domain signals to extract relevant electromechanical mode information, illustrating that, under certain conditions, typical STATCOM TS models can yield too optimistic results, which may lead to errors in power system planning and operation.
Lasing properties of InGaAsP buried heterojunction lasers grown on a mesa substrate (1982)

The lasing properties of InGaAsP crescent-shape mesa substrate buried heterojunction (CMSB) lasers emitting at 1.3 μm are described. Threshold currents as low as 20 mA have been observed with a temperature sensitivity T0 = 97 °C. An external differential quantum efficiency (two facets) of up to 54% was observed. This combination of the characteristics is directly attributed to the device structure which is specially designed to decrease lateral leakage current. Single transverse and longitudinal mode operation was realized with output powers of at least 5 mW per facet.
A Novel Homotopy Perturbation Transform Algorithm for Linear and Nonlinear System of Partial Differential Equations (2011)

In this paper, a Homotopy Perturbation Transform Algorithm (HPTA) which is based on the Homotopy Perturbation Method (HPM) is introduced for the approximate solution of the linear and nonlinear system of partial differential equations. Illustrative examples are included to demonstrate the high accuracy and fast convergence of proposed new algorithm.
ATRON Robots: Versatility from Self-Reconfigurable Modules (2007)

Traditional fixed morphology robots are limited to purely functional adaptation and thereby to a limited range of applications. In contrast modular self-reconfigurable robots can dynamically and autonomously change both their function and morphology to meet new demands of changing tasks. Therefore, self-reconfigurable robots have the potential to become highly versatile. This paper documents and discusses the application versatility of self-reconfigurable robots in general and of the ATRON system in particular. We present a range of different self-reconfigurable robots assembled from the ATRON base module. The robot's ability includes locomotion (snake, car, and walker), manipulation of objects (serial manipulator, conveyer belt) and autonomous change of functionality and shape (locomotion configurations, many-module shape-change). We also demonstrate the structure of simple anatomical building blocks (bones, muscles, etc.) which we envision can be assembled into more complex robots of future miniaturized modules.
Multi-lane detection in urban driving environments using conditional random fields (2013)

Over the past few decades, the need has arisen for multi-lane detection algorithms for use in vehicle safety-related applications. In this paper we propose a new multi-lane detection algorithm that works well in urban situations. This algorithm detects four lane marks, including driving lane marks and adjacent lane marks. Conventional research assumes that lanes are parallel. In contrast, our approach does not require this assumption, thus enabling the algorithm to manage various non-parallel lane situations, such as are found at intersections, in splitting lanes, and in merging lanes. To detect multi-lane marks successfully in the absence of parallelism, we adopt Conditional Random Fields (CRFs), which are strong models for solving multiple association tasks. We show that CRFs are very effective tools for multi-lane detection because they find an optimal association of multiple lane marks in complex and challenging urban road situations. Through simulations, and by using video sequences with 752-480 resolution and Caltech Lane Datasets with runtime rates of 30 fps, we verify that our algorithm successfully detects non-parallel lanes as well as parallel lanes appearing in urban streets.
Structural and mechanistic studies of tunable, stable, fast multi-cobalt water oxidation catalysts (2011)

New multi-cobalt-containing polyoxometalates (POMs) are soluble, fast and tunable water oxidation catalysts (WOCs). We report additional studies of [Co<sub>4</sub>(H<sub>2</sub>O)<sub>2</sub>(PW<sub>9</sub>O<sub>34</sub>)<sub>2</sub>]<sup>10-</sup> (1), a very fast, soluble and oxidative stable WOC: new kinetics data further indicate that Co<sup>2+</sup> is not kinetically important in water oxidations catalyzed by 1. Second, we report a new WOC, [{Co<sub>4</sub>(ì-OH)(H<sub>2</sub>O)<sub>3</sub>}(Si<sub>2</sub>W<sub>19</sub>O<sub>70</sub>)]<sup>11-</sup> that coexists in a 1:1 ratio in the solid state (2a and 2b), and while it is oxidatively stable, it is not hydrolytically stable, rearranging to [Co(H<sub>2</sub>O)SiW<sub>11</sub>O<sub>39</sub>]<sup>6-</sup> in aqueous solution. All these studies provide insights relating structural, electronic and other features of these WOCs to their reactivity and stability.
(1,3-Dithiolan-2-YL)Acetonitrile: A Versatile Three-Carbon Building Block1 (1974)

Abstract Recently, in connection with other work, we required cyano-acetaldehyde as a usefully functionalized three-carbon building block. Although first reported in 18893 as an isolable compound, cyanoacetaldehyde has appeared in the literature only as various derivatives since that time.4 Indeed, in these laboratories, all attempts to prepare cyanoacetaldehyde have failed because of its great instability.
Integration of Natural User Interface in a Real-World Environment (2015)

The use of Natural User Interface in a real-world environment is explored by taking the example of a classroom in a government (public) school in a developing country such as India. Problems such as lack of infrastructure and inability to instill interest among students are addressed. A Microsoft Kinect based application was developed to demonstrate the use of Natural User Interface in such a classroom. The application maps Natural User Interface elements onto a Graphical User Interface and the application logic. The body gestures, distance from motion sensing device, and camera feed completely control the application, its look and feel, and the computations performed by it. The work performed, the main innovation and the salient aspects of the application, implemented as a student project, are presented.
Intestinal lysozyme liberates Nod1 ligands from microbes to direct insulin trafficking in pancreatic beta cells (2019)

Long-range communication between intestinal symbiotic bacteria and extra-intestinal organs can occur through circulating bacterial signal molecules, through neural circuits, or through cytokines or hormones from host cells. Here we report that Nod1 ligands derived from intestinal bacteria act as signal molecules and directly modulate insulin trafficking in pancreatic beta cells. The cytosolic peptidoglycan receptor Nod1 and its downstream adapter Rip2 are required for insulin trafficking in beta cells in a cell-autonomous manner. Mechanistically, upon recognizing cognate ligands, Nod1 and Rip2 localize to insulin vesicles, recruiting Rab1a to direct insulin trafficking through the cytoplasm. Importantly, intestinal lysozyme liberates Nod1 ligands into the circulation, thus enabling long-range communication between intestinal microbes and islets. The intestine-islet crosstalk bridged by Nod1 ligands modulates host glucose tolerance. Our study defines a new type of inter-organ communication based on circulating bacterial signal molecules, which has broad implications for understanding the mutualistic relationship between microbes and host.
Studies on the Azaindolizine Compounds. XII. Alkyl Rearrangement of 5-Methyl-7-alkoxy-s-triazolo [1, 5-a] pyrimidines. (1963)

5-Methyl-7-methoxy-s-triazolo [1, 5-a] pyrimidine (IVa) was prepared by the reaction of the 7-chloro compound III with sodium methoxide at below room temperature. The property of the 7-alkoxy derivatives (IVa and IVb) was examined and it was discovered that the alkyl group of these derivatives undergoes rearrangement to the ring nitrogen at 3- and 4-positions. In order to determine the structure of the products being obtained by above rearrangement, the reaction of ethyl acetoacetate with 5-alkylaminos-triazoles (XIVa and XIVb) and 4-alkyl-5-aminos-triazoles (XVa and XVb) which were prepared from 1-alkyl-2-aminoguanidinium sulfates (XIIa and XIIb), was investigated.
A233 CHARACTERIZATION OF THE DUODENAL MICROBIOME IN PEDIATRIC CELIAC AND INFLAMMATORY BOWEL DISEASE PATIENTS (2022)

Abstract Background Both Celiac disease (CE) and inflammatory bowel disease (IBD) are lifelong gastrointestinal tract (GIT) disorders. CE is an autoimmune disorder triggered by gluten consumption and can result in small intestine villus atrophy, crypt hyperplasia and epithelial permeability, while IBD is characterized by chronic, reoccurring inflammation and ulcers in the GIT. There is increasing evidence linking GIT microbes to both CE and IBD pathogenesis. Studies have also shown that CE patients are at increased risk of developing IBD, suggesting a possible link between these diseases. The duodenum can be affected in both CE and IBD, but it is understudied as compared to other GIT regions. Aims We thus aimed to characterize the duodenal microbiome of pediatric CE, IBD and control patients (n=76, 48 and 57 respectively) and hypothesized that the composition of microbes would vary between each diagnostic group. Methods We used mucosal luminal interface aspirates collected during upper endoscopy at the Children’s Hospital of Eastern Ontario. Metagenomic DNA was extracted from these samples and bacterial taxa was characterized by sequencing the V6 hypervariable region of the 16S rRNA gene. Results Control, CE, and IBD duodenal microbiotas showed no apparent differences in either α-diversity or β-diversity. However, we identified several significant differences between the relative abundances of specific taxa in these three patient groups. In particular, Atopobium parvulum was found to be enriched in Crohn’s disease samples when compared to non-IBD controls. There was also a trend for higher Bacteroides, Lactobacillus, Parabacteroides and Staphylococcus in CE patient MLI aspirates. These results are similar to what has been previously reported in CE patients. Finally, trends found in the duodenal MLI aspirates are more consistent with results previously found in the salivary microbiome in CD patients as opposed to studies of the large intestine. Conclusions This work provides unique insight into the microbial composition at the duodenum; a GIT region that has not been fully characterized in CE or IBD. Funding Agencies CIHRGenome Canada
Design for reliability of multi-layer stretchable interconnects (2014)

In this investigation, the electrical performance and reliability of multi-layer stretchable metal interconnects are evaluated using numerical simulations and experimental analysis. The numerical results show that the bi-layer design of stretchable interconnects have similar mechanics when compared to single layer interconnect structures. In contrast, interconnects configured in an in-plane stacked arrangement exhibit increased equivalent plastic strain during elongation, and consequently support less stretching. Our experimental results support these numerical findings. Maximum stretchability approaches ~150% elongation for single layer and bi-layer interconnects. In addition, fatigue experiments at 60% elongation show that the bi-layer design of stretchable interconnects have life cycles three orders of magnitude higher than the in-plane stacked arrangement of stretchable interconnects.
Candidate mutations for early-onset lung cancer by family genome sequencing (2011)

Early-onset lung cancer has been studied as a rare, but distinct, sub-type of lung cancer. Genome-wide association studies (GWAS) have linked several genes with this form of malignancy. We sequenced the genomes of a family quartet in which one of the offspring was diagnosed with early-onset lung cancer at about 48 years of age. The family has a history of heavy smoking and the father had in the past been diagnosed with head and neck cancer. The DNA source was blood, which leads us to concentrate our analysis on Mendelian inheritance models. To make the inheritance pattern explicit, we establish the parental origin of the offspring’s genomes through phasing of their chromosomes. This helps identify whether mutations in the proband came from the father or the mother. More than 18 million sequence variants were initially identified in the proband through comparison to the hg19 reference genome. We reduce this list to fewer than 200 potentially functional variants (e.g. single nucleotide variations and short indels) present in the genomes of the proband and at least one parent, by applying a series of filters. We refine the list of candidate mutations further by comparison to gene candidates from GWAS studies and genes that are mutated in lung cancer tissue as recorded by The Cancer Genome Atlas. The results of our analysis are discussed and conclusions about possible causative mutations for early-onset lung cancer are drawn.
Detection of metastases in breast cancer: Is whole body PET/MR better than PET/CT? (2014)

11002 Background: Whole body (WB)PET/CT is commonly utilized in breast cancer (BC) patients (pts). Limitations include assessment of treatment response in bone metastases (mets), high physiologic uptake in brain and liver, and cumulative radiation exposure. The site of mets can have prognostic and therapeutic implications. PET/MR, an exciting new hybrid technology, delivers less radiation than PET/CT. Our aim was to compare the differences in metastatic lesion detection using PET/CT and PET/MR in all BC subtypes. Methods: Pts who had WB PET/CT for staging and assessment of treatment response also had WB PET/MR after a single 18-FDG injection. PET/MR and PET/CT images were each read by a radiologist blinded to prior exams or reports. The number of mets per organ was recorded. 2 experienced radiologists unblinded to imaging and pathology reports served as the gold standard. Clinical data were obtained. Trial accrual is ongoing. Results: 48 pts underwent PET/CT and PET/MR (28 MBC, 5 neoadjuvant & 15 adjuvant setting). Median age was 48; range 31-79 with 31 ER+/HER2-, 9 ER+/HER2+, 2 ER-/HER+, 5 ER-/HER2-, 1 unknown. 11 pts had no evidence of mets. In remaining 37 pts, PET/MR and/or PET/CT detected bone, liver, or brain mets in 23, 9 and 5 pts, respectively; some patients had ≥1 metastatic site. PET/MR accurately detected 1 bone (ER+/HER2), 3 liver (ER+/HER2-) and 5 brain lesions (2 ER+/HER2-, 2ER-/HER2+, 1ER+/HER2+) in 8 unique pts that were not identified on PET/CT. 2 liver and 2 brain mets identified on PET/MR were previously unknown. PET/MR accurately reported treated bone lesions in 10 pts. Per organ system, there were more false neg and false pos with PET/CT (Table). Conclusions: Our preliminary data suggest that PET/MR may be more sensitive and specific than PET/CT in detecting mets in breast cancer. Prospective studies of PET/MR are warranted to determine whether early detection of mets, including occult brain mets in HER2+ pts, impacts survival. Organ (N)a # Pts with concordant PET/CT & PET/MR findings # Pts with false (+) on PET/CT # Pts with false (-) on PET/CT Bone (23) b 10 9 2 Lung (5) 2 2 1 Pleura (5) 4 1 0 Nodes (axilla + other) (19) 9 6 4 Liver (9) 5 1 3 Brain (5) 0 0 5 aSome pts had ≥1 metastatic site b In 2 pts, neither modality accurately detected the # lesions.
SEARCHING FOR MEANS TO STIMULATE INJURED NERVE REGENERATION USING NOVEL CELL TECHNOLOGIES (2015)

The review addresses the development of cell technologies designed to stimulate injured nerve regeneration, including original and published results. The experimental use of dissociated cells derived from embryonic primordiums of different neural system organs and of mesenchymal stem cells to stimulate nerve regeneration is discussed. The need for further basic research of grafted cells fate and their effects on recipient’s nerve fiber growth is emphasized.
Antibodies to Variant Surface Antigens ofPlasmodium falciparum–Infected Erythrocytes Are Associated with Protection from Treatment Failure and the Development of Anemia in Pregnancy (2009)

Higher levels of both IgG antibodies to VSA-PAM and opsonizing antibodies, a functional measure of immunity, correlate with parasite clearance and less anemia in pregnancy malaria.
Effects of Sustained Insulin-Induced Hypoglycemia on Cardiovascular Autonomic Regulation in Type 1 Diabetes (2005)

Effects of hypoglycemia on cardiac autonomic regulation may contribute to the occurrence of adverse cardiac events. This study assessed the effects of sustained hyperinsulinemic hypoglycemia on cardiovascular autonomic regulation in type 1 diabetic patients and their nondiabetic counterparts. The study consisted of 16 type 1 diabetic patients and 8 age-matched healthy control subjects who underwent euglycemic and hypoglycemic clamp procedures in a random order. Heart rate variability was measured from continuous electrocardiogram recordings by time and frequency domain methods, along with Poincare plot analysis during both a hyperinsulinemic-euglycemic and hypoglycemic clamp at three different glucose levels (4.5-5.5, 3.0-3.5, and 2.0-2.5 mmol/l). Controlled hypoglycemia resulted in an increase of supine heart rate in both the diabetic patients (from 72 +/- 9 to 80 +/- 11 bpm, P < 0.01) and the control subjects (from 59 +/- 5 to 65 +/- 5 bpm, P < 0.05) and progressive reductions of the high-frequency spectral component and beat-to-beat heart rate variability (SD1; P < 0.05 in the diabetic patients and P < 0.01 in control subjects). No significant changes in heart rate variability occurred during the euglycemic clamp. We conclude that hypoglycemia results in a reduction of cardiac vagal outflow in both diabetic and nondiabetic subjects. Altered autonomic regulation may contribute to the occurrence of cardiac events during hypoglycemia.
Highly accurate surface reconstruction for deflectometry (2012)

Deflectometry is a simple but powerful technique to test and measure specular surfaces, where the reflection angles from a test surface reveal local slopes, and thereby, optical imperfections. The slope data can be differentiated into curvature data, enabling sensitivities in the nm range [1]; on the other hand, integrating them into shape data is much more difficult, as the measured surface must have continuous slopes and the geometry of the measurement must be extremely well characterised. Even so, deflectometric surface measurements to less than 1 μm uncertainty are rare. This is one (and possibly the only) reason why deflectometry cannot yet compete with interferometry, although it is in principle much more versatile.