Miracle-dz/UniFAR-FTUs huggingface dataset:
ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

Synthetic biology and metabolic engineering rely on computational search tools for predictions of novel biosynthetic pathways to industrially important compounds, many of which are derived from aromatic amino acids. Pathway search tools vary in their scope of covered reactions and compounds, as well as in metrics for ranking and evaluation. In this work, we present a new computational resource called ARBRE: Aromatic compounds RetroBiosynthesis Repository and Explorer. It consists of a comprehensive biochemical reaction network centered around aromatic amino acid biosynthesis and a computational toolbox for navigating this network. ARBRE encompasses over 28’000 known and 100’000 novel reactions predicted with generalized enzymatic reactions rules and over 70’000 compounds, of which 22’000 are known to biochemical databases and 48’000 only to PubChem. Over 1,000 molecules that were solely part of the PubChem database before and were previously impossible to integrate into a biochemical network are included into the ARBRE reaction network by assigning enzymatic reactions. ARBRE can be applied for pathway search, enzyme annotation, pathway ranking, visualization, and network expansion around known biochemical pathways to predict valuable compound derivations. In line with the standards of open science, we have made the toolbox freely available to the scientific community at http://lcsb-databases.epfl. ch/arbre/. We envision that ARBRE will provide the community with a new computational toolbox and comprehensive search tool to predict and rank pathways towards industrially important aromatic compounds.
Experience with directional couplers for partial discharge measurements on rotating machines in operation

Manitoba Hydro applied directional couplers for on-line partial discharge measurements on selected rotating machines beginning in 1981. With the instrumentation available at that time the measurement was vulnerable to the effects of noise external to the machine. There have been improvements in the available coupling capacitors which have allowed selection of more optimum measuring locations. In addition, new instrumentation has become available which allows some of the more serious noise problems to be overcome. The paper describes these developments as well as some of the stator winding problems which have been detected.
Construction safety: economics, information and management involvement

In order to induce top management of construction companies in Israel to become involved in safety, the present research undertook to prove that in Israel, too, uninsured accident costs are very high. Through in-depth interviews of 50 site managers concerning 210 accidents, complementary interviews with other officials in construction and insurance companies, study of records, and conduct of direct observations of accidents after they occurred, a conclusion contradicting the accepted view in insurance circles is reached. The research establishes that uninsured costs in construction companies with an average safety performance record amount to a mere 0.76% of the payroll. In a parallel research in large, developed companies in the USA, existing safety measurement methods feeding the information system were studied.
A CAD-oriented analytical model for the losses of general asymmetric coplanar lines in hybrid and monolithic MICs

New analytical approximations are derived for the conductor losses of asymmetric coplanar waveguides (ACPW) and coplanar striplines (ACPS) on a finite-thickness dielectric substrate. The expressions hold for lines whose metallizations have thickness much smaller than the slot and strip widths, but suitably larger than the skin penetration depth at the operating frequency. The derivation is based on an extension of the conformal mapping approach formerly proposed by Owyang and Wu (1958) for symmetric lines in air. Comparisons with published data from quasistatic or full-wave numerical analyses are presented to validate the expressions derived for both the symmetric and the asymmetric case. The analytical characterization presented in the paper is well suited for inclusion into CAD codes for MMIC design. >
Predicting Beliefs from NPC Dialogues

Game designers and developers benefit from gathering data from players; however, interrupting play with questionnaires can harm experience. Previous work has suggested that embedding questionnaires into games, such as through dialogue choices when interacting with non-player characters (NPCs) can help, but there is no evidence that dialogue choices can model the real-world beliefs of players. In this study we demonstrate two methods of successfully predicting responses to validated scales of sexist beliefs from NPC dialogues that do not differ in their resulting narrative engagement. Our findings open opportunities for better tailoring games and game experiences by modeling players through their in-game interactions.
A Maximum A Posteriori Relaxation For Clustering The Labeled Stochastic Block Model

We consider the clustering problem for the labeled stochastic block model (LSBM) with non-uniform class priors. We introduce a novel relaxation of the maximum a posteriory (MAP) estimator for the cluster labels and develop an algorithm for the numerical solution of this relaxation, assuming that the number of clusters, the class priors, and the label distributions are known in advance. Semi-supervised operation is enabled by allowing each node to have a distinct prior. Numerical experiments confirm that our method outperforms state-of-the-art approaches in terms of clustering accuracy.
Numerical Modeling and Simulation of Pressure Wave in Combination Electronic Unit Pump High Pressure Pipeline

High pressure (HP) fuel pipeline is one of the major components of Combination Electronic Unit Pump (CEUP) diesel fuel injection system and has significant contribution in building up of high pressure required during fuel injection cycle. A MATLAB numerical model of pressure wave inside HP fuel pipeline of CEUP system using damped wave equation has been developed in MATLAB to study and simulate pressure wave propagation through fuel pipeline at various operating conditions of diesel engine. Finite Difference method has been applied to model and simulate pressure equation at various equidistant locations of fuel pipeline. Dynamic variations of fuel properties as a function of varying pressure have also been incorporated. The MATLAB model has been validated by comparing simulated pressures with those of experimentally validated AMESim numerical model of CEUP fuel injection system. Quantitative comparisons were also done using Root Mean Square Error (RMSE) and Index of Agreement (IA). Results show that MATLAB numerical model is quite accurate especially at low cam rotational speeds and low cam angles.
TIME DOMAIN ANALYSIS OF CARBON NANOTUBE INTERCONNECTS BASED ON DISTRIBUTED RLC MODEL

This paper introduces an accurate analysis of time domain response of carbon nanotube (CNT) interconnects based on distributed RLC model that takes the effect of both the series resistance and the output parasitic capacitance of the driver into account. Using rigorous principle calculations, accurate expressions for the transfer function of these lines and their time domain response have been presented. It has been shown that the second-order transfer function cannot represent the distributed behavior of the long CNT interconnects, and the fourth-order approximation offers a better result. Also, the time response of a driven long CNT interconnect versus length and diameter have been studied. The obtained results show that the overshoot increases and the time delay decreases with increasing the CNT diameter, such that with the diameter value of 10 nm for a 3.3 mm CNT interconnect, the maximum overshoot value reaches about 95% of the amplitude of the driver input. On the contrary, the overshoot increases and the time delay decreases with decreasing the length of the CNT, such that with the length value of 1 mm for a 5 nm diameter CNT interconnect, the maximum overshoot reaches about 90% of the amplitude of the driver input.
The construction of missile guidance codes resistant to random interference

Many types of missiles are guided by a finite set of distinct commands radioed from the ground in the form of a time-sequence of RF pulses. The command information is contained in the n − 1 time spacings between successive pulses in a group of size n, and is encoded and decoded by means of multitapped delay lines combined with AND gates. This paper discusses the problem of encoding command information (i.e., selecting the time spacings between pulses) so that m false pulses (m $$ n − 2) cannot combine with the n true pulses in any way to form a false command. Although it is very easy to state the restrictions that must be imposed on the time spacings between the pulses in the different commands, no general methods exist for finding, among codes satisfying these restrictions, those codes in which the longest command is as short as possible. This paper presents certain lower bounds, together with a few empirically derived codes approaching these lower bounds. The relationship between these codes and the well-known error-correcting binary codes of information theory is discussed in an appendix.
CT Angiography Manual Multiplanar Vessel Diameter Measurement vs. Semiautomated Perpendicular Area Minimal Caliber Computation of Internal Carotid Artery Stenosis

Objective: To determine the diagnostic agreement of CT angiography (CTA) manual multiplanar reformatting (MPR) stenosis diameter measurement and semiautomated perpendicular stenosis area minimal caliber computation of extracranial internal carotid artery (ICA) stenosis. Methods: We analyzed acute cerebral ischemia CTA at our tertiary stroke center in a 12-month period. Prospective NASCET-type stenosis grading for each ICA was independently performed using (1) MPR to manually determine diameters and (2) perpendicular stenosis area with minimal caliber semiautomated computation to grade luminal constriction. Corresponding to clinically relevant NASCET strata, results were grouped into severity ranges: normal, 1–49%, 50–69%, and 70–99%, and occlusion. Results: We included 647 ICA pairs from 330 patients (median age of 74 [66–80, IQR]; 38–92 years; 58% men; median NIHSS 4 [1–9, IQR]). MPR diameter and semiautomated caliber measurements resulted in stenosis grades of 0–49% in 143 vs. 93, 50–69% in 29 vs. 27, 70–99% in 6 vs. 14, and occlusion in 34 vs. 34 ICAs (p = 0.003), respectively. We found excellent reliability between repeated manual CTA assessments of one expert reader (ICC = 0.997; 95% CI, 0.993–0.999) and assessments of two expert readers (ICC = 0.972; 95% CI, 0.936–0.988). For the semiautomated vessel analysis software, both intrarater reliability and interrater reliability were similarly strong (ICC = 0.981; 95% CI, 0.952–0.992 and ICC = 0.745; 95% CI, 0.486–0.883, respectively). However, Bland–Altman analysis revealed a mean difference of 1.6% between the methods within disease range with wide 95% limits of agreement (−16.7–19.8%). This interval even increased with exclusively considered vessel pairs of stenosis ≥1% (mean 5.3%; −24.1–34.7%) or symptomatic stenosis ≥50% (mean 0.1%; −25.7–26.0%). Conclusion: Our findings suggest that MPR-based diameter measurement and the semiautomated perpendicular area minimal caliber computation methods cannot be used interchangeably for the quantification of ICA steno-occlusive disease.
Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma

Burkitt lymphoma (BL) accounts for the majority of pediatric non-Hodgkin lymphomas (NHL) and is relatively rare but significantly more lethal when diagnosed in adults. The global incidence is highest in Sub-Saharan Africa, where Epstein-Barr virus (EBV) positivity is observed in 95% of all tumors. Both pediatric (pBL) and adult (aBL) cases are known to share some driver mutations, for example MYC translocations, which are seen in > 90% of cases. Sequencing efforts have identified many common somatic alterations that cooperate with MYC in lymphomagenesis with approximately 30 significantly mutated genes (SMG) reported thus far. Recent analyses revealed non-coding mutation patterns in pBL that were attributed to aberrant somatic hypermutation (aSHM). We sought to identify genomic and molecular features that may explain clinical disparities within and between aBL and pBL in an effort to delineate BL subtypes that may allow for the stratification of patients with shared pathobiology. Through comprehensive sequencing of BL genomes, we found additional SMGs, including more genetic features that associate with tumor EBV status, and established three new genetic subgroups that span pBL and aBL. Direct comparisons between pBL and aBL revealed only marginal differences and the mutational profiles were consistently better explained by EBV status. Using an unsupervised clustering approach to identify subgroupings within BL and diffuse large B-cell lymphoma (DLBCL), we have defined three genetic subgroups that predominantly comprise BL tumors. Akin to the recently defined DLBCL subgroups, each BL subgroup is characterized by combinations of common driver mutations and non-coding mutations caused by aSHM. Two of these subgroups and their prototypical genetic features (ID3 and TP53) had significant associations with patient outcomes that were different among the aBL and pBL cohorts. These findings highlight not only a shared pathogenesis between aBL and pBL, but also establish genetic subtypes within BL that serve to delineate tumors with distinct molecular features, providing a new framework for epidemiological studies, and diagnostic and therapeutic strategies.
Effects of Climate Change on the Distribution of Akebia quinata

Akebia quinata, also known as chocolate vine, is a creeping woody vine which is used as Chinese herbal medicine, and found widely distributed in East Asia. At present, its wild resources are being constantly destroyed. This study aims to provide a theoretical basis for the resource protection of this plant species by analyzing the possible changes in its geographic distribution pattern and its response to climate factors. It is the first time maximum entropy modeling (MaxEnt) and ArcGIS software have been used to predict the distribution of A. quinata in the past, the present, and the future (four greenhouse gas emission scenarios, namely, SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). Through the prediction results, the impact of climate change on the distribution of A. quinata and the response of A. quinata to climate factors were analyzed. The results showed that the most significant climatic factor affecting the distribution pattern of A. quinata was the annual precipitation. At present, the suitable distribution regions of A. quinata are mainly in the temperate zone, and a few suitable distribution regions are in the tropical zone. The medium and high suitable regions are mainly located in East Asia, accounting for 51.1 and 81.7% of the worldwide medium and high suitable regions, respectively. The migration of the geometric center of the distribution regions of A. quinata in East Asia is mainly affected by the change of distribution regions in China, and the average migration rate of the geometric center in each climate scenario is positively correlated with the level of greenhouse gas emission scenario.
COP1 promotes seed germination by destabilizing RGA-LIKE2 (RGL2) in Arabidopsis

Under favorable moisture, temperature and light conditions, gibberellin (GA) biosynthesis is induced and triggers seed germination. A major mechanism by which GA promotes seed germination is by promoting the degradation of the DELLA protein RGL2, a major repressor of germination in Arabidopsis seeds. Analysis of seed germination phenotypes of constitutively photomorphogenic 1 (cop1) mutants and complemented COP1-OX/cop1-4 lines in response to GA and paclobutrazol (PAC) suggested a positive role for COP1 in seed germination and a relation with GA signaling. cop1-4 mutant seeds showed PAC hypersensitivity, but transformation with a COP1 overexpression construct rendered them PAC insensitive, with a phenotype similar to that of rgl2 mutant (rgl2-SK54) seeds. Furthermore, cop1-4 rgl2-SK54 double mutants showed a PAC-insensitive germination phenotype like that of rgl2-SK54, identifying COP1 as an upstream negative regulator of RGL2. COP1 interacts directly with RGL2 and in vivo this interaction is strongly enhanced by SPA1. COP1 directly ubiquitinates RGL2 to promote its degradation. Moreover, GA stabilizes COP1 with consequent RGL2 destabilization. By uncovering this COP1-RGL2 regulatory module, we reveal a novel mechanism whereby COP1 positively regulates seed germination and controls the expression of germination-promoting genes.
Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara

Bacteria colonize specific niches in the animal gut. However, the genetic basis of these associations is often unclear. The proteobacterium Frischella perrara is a widely distributed gut symbiont of honey bees. It colonizes a specific niche in the hindgut and causes a characteristic melanization response. Genetic determinants required for the establishment of this association, or its relevance for the host, are unknown. Here, we independently isolated three point mutations in genes encoding the DNA-binding protein integration host factor (IHF) in F. perrara. These mutants abolished the production of an aryl polyene metabolite causing the yellow colony morphotype of F. perrara. Inoculation of microbiota-free bees with one of the mutants drastically decreased gut colonization of F. perrara. Using RNAseq we found that IHF affects the expression of potential colonization factors, including genes for adhesion (Type 4 pili), interbacterial competition (Type 6 secretion systems), and secondary metabolite production (colibactin and aryl polyene biosynthesis). Gene deletions of these components revealed different colonization defects depending on the presence of other bee gut bacteria. Interestingly, one of the T6SS mutants did not induce the scab phenotype anymore, despite colonizing at high levels, suggesting an unexpected role in bacteria-host interaction. IHF is conserved across many bacteria and may also regulate host colonization in other animal symbionts.
A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression

Used widely for genome editing in human cells, plants and animals, CRISPR-Cas enzymes including Cas9 and Cas12 provide RNA-guided immunity to microbes by targeting foreign DNA sequences for cleavage. We show here that the native activity of CRISPR-Cas12c protects bacteria from phage infection by binding to DNA targets without cleaving them, revealing that antiviral interference can be accomplished without chemical attack on the invader or general metabolic disruption in the host. Biochemical experiments demonstrate that Cas12c is a site-specific ribonuclease capable of generating mature CRISPR RNAs (crRNAs) from precursor transcripts. Furthermore, we find that crRNA maturation is essential for Cas12c-mediated DNA targeting. Surprisingly, however, these crRNAs direct double-stranded DNA binding by Cas12c using a mechanism that precludes DNA cutting. Cas12c’s RNA-guided DNA binding activity enables robust transcriptional repression of fluorescent reporter proteins in cells. Furthermore, this naturally DNase-free Cas12c enzyme can protect bacteria from lytic bacteriophage infection when targeting an essential phage gene. Together these results show that Cas12c employs targeted DNA binding to provide anti-viral immunity in bacteria, providing a native DNase-free pathway for transient antiviral immunity.
Robust trajectory control of underwater vehicles

The Deep Submergence Laboratory at the Woods Hole Oceanographic Institution is currently developing supervisory control system methodologies for underwater vehicles and manipulators. These technologies are currently being applied to Several tethered systems under development at the laboratory, however much of the work is directly applicable to untethered systems as well. Specific areas under investigation include man-machine interface design, control theoretic aspects of vehicle and manipulator control, and navigation sensors. The design of the closed-loop control system is a primary issue for any underwater vehicle that is not controlled manually. Precise trajectory control of all vehicles movements is particularly difficult due to the nonlinear, uncertain nature of the dynamics of underwater systems. A new control system design methodology called sliding control has been shown to deal with these difficult problems very effectively. In this paper, methodology and results from simulation and actual tests in the water are reviewed.
A modified two‐strip monopole antenna for WiFi and WiMAX applications

This article reports a modification of two‐strip monopole antenna, which was an undergraduate final year project. The modified antenna uses a thicker substrate when compared with the original design while maintaining the monopole radiation characteristics at the WiFi frequency bands of 2.4 and 5 GHz. One of the significant improvements of the antenna is the inclusion of the mobile WiMAX frequency band at 3.5 GHz. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 2884–2886, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24801
A workstation for manipulation of micro objects

The micromanipulation of tiny mechanical and biological objects, with its wide range of application, is becoming a research field of strong interest both for university and industry. Micromechatronics and robotics may be capable of improving present micromanipulation techniques and even of opening new application areas. In this paper, after a short illustration of the state of the art, a critical analysis of the problems to be solved for reducing current limitations and improving micromanipulation devices is presented. Finally, the main features of a workstation for micromanipulation of micro-objects which is being developed in the authors' laboratory are discussed.
Single stage, high power factor, lamp ballast

Unlike conventional ballasts requiring two cascaded stages, a new lamp ballast achieves near unity input power factor and high frequency sinusoidal lamp current in a single power conversion stage. A new discontinuous inductor current mode (DICM) of input inductor makes this possible by separating the input current shaping from high frequency output lamp ballasting function. The high efficiency is further enhanced by soft switching improvement, which is provided naturally through lagging current of the output resonant matching network. Design equations and experimental results verify all the advantages of the new lamp ballast. <<ETX>>