Miracle-dz/UniFAR-FTUs huggingface dataset:
Tangent-Space Regularization for Neural-Network Models of Dynamical Systems

This work introduces the concept of tangent space regularization for neural-network models of dynamical systems. The tangent space to the dynamics function of many physical systems of interest in control applications exhibits useful properties, e.g., smoothness, motivating regularization of the model Jacobian along system trajectories using assumptions on the tangent space of the dynamics. Without assumptions, large amounts of training data are required for a neural network to learn the full non-linear dynamics without overfitting. We compare different network architectures on one-step prediction and simulation performance and investigate the propensity of different architectures to learn models with correct input-output Jacobian. Furthermore, the influence of $L_2$ weight regularization on the learned Jacobian eigenvalue spectrum, and hence system stability, is investigated.
A Heuristic for Variable Re-Entrant Scheduling Problems

Flexible Manufacturing Systems (FMSs) need a scheduler to provide timing instructions for the operations of different products. Previous work has presented heuristics for fixed-order 2-re-entrant scheduling problems; where products visit a re-entrant machine exactly two times for production. We propose an extension to this scheduling model, and an extension to the scheduling heuristic, that allows jobs to move along different flows on re-entrant machines; i.e. jobs can visit the re-entrant machine once or twice. An FMS that requires such variable re-entrance with fixed-order output is a Large Scale Printer (LSP). The scheduling problem in an lsp is modeled as a variable re-entrance flowshop with relative due dates and sequence-dependent setup times, with a fixed order output. We show that out-of-order input of products can be beneficial to the scheduling quality in variable re-entrance scheduling. A fixed re-entrant heuristic is extended such that it orders operations on the re-entrant machine to minimize the completion time of variable re-entrant job sets. The resulting heuristic produces good quality schedules for variable re-entrant job sets without losing schedule quality for fixed re-entrant job sets.
Genomic Variability among Field Isolates and Laboratory-Adapted Strains of Leptospira borgpetersenii Serovar Hardjo

Leptospira borgpetersenii serovar Hardjo colonizes cattle kidneys and may occasionally infect humans and other mammals. Strains belonging to two clonal subtypes (types A and B) with marked differences in their pathogenicity in the hamster experimental model have been described for this serovar. Such differences have been attributed to point mutations in individual genes, although those genes have not yet been characterized. In order to better understand genetic variability among L. borgpetersenii serovar Hardjo isolates, we sequenced and compared the genomes of two laboratory-adapted strains and three abattoir-derived field isolates of L. borgpetersenii serovar Hardjo. Relatively low genetic variability was observed within isolates of the same subtype, with most of the mutations of moderate or high impact found in the laboratory-adapted isolates. In contrast, several differences regarding gene content and genetic variants were observed between the two subtypes. Putative type-specific genes appear to encode proteins associated with functions that are critical for infection. Some of these genes seem to be involved in transcriptional regulation, possibly leading to a distinct regulatory pattern in each type. These results show that changes in regulatory mechanisms, previously suggested to be critical during Leptospira speciation, may occur in L. borgpetersenii. In addition, the bioinformatics methodology used in this study for variant calling can be useful to other groups working with nonmodel prokaryotic organisms such as Leptospira species.
Genomic Selection in Preliminary Yield Trials in a Winter Wheat Breeding Program

Genomic prediction (GP) is now routinely performed in crop plants to predict unobserved phenotypes. The use of predicted phenotypes to make selections is an active area of research. Here, we evaluate GP for predicting grain yield and compare genomic and phenotypic selection by tracking lines advanced. We examined four independent nurseries of F3:6 and F3:7 lines trialed at 6 to 10 locations each year. Yield was analyzed using mixed models that accounted for experimental design and spatial variations. Genotype-by-sequencing provided nearly 27,000 high-quality SNPs. Average genomic predictive ability, estimated for each year by randomly masking lines as missing in steps of 10% from 10 to 90%, and using the remaining lines from the same year as well as lines from other years in a training set, ranged from 0.23 to 0.55. The predictive ability estimated for a new year using the other years ranged from 0.17 to 0.28. Further, we tracked lines advanced based on phenotype from each of the four F3:6 nurseries. Lines with both above average genomic estimated breeding value (GEBV) and phenotypic value (BLUP) were retained for more years compared to lines with either above average GEBV or BLUP alone. The number of lines selected for advancement was substantially greater when predictions were made with 50% of the lines from the testing year added to the training set. Hence, evaluation of only 50% of the lines yearly seems possible. This study provides insights to assess and integrate genomic selection in breeding programs of autogamous crops.
Clinical characteristics and treatment outcomes among respiratory syncytial virus (RSV)-infected hematologic malignancy and hematopoietic stem cell transplant recipients receiving palivizumab

Abstract Palivizumab has been used to treat respiratory syncytial virus (RSV)-infected hematologic malignancy patients at our institution based on limited published data. We conducted this retrospective study to evaluate clinical outcomes and mortality rates of RSV-infected hematologic malignancy patients from 2007 to 2016. A total of 67 patients (19 received palivizumab and 47 received supportive care) were identified. Palivizumab-treated patients had a significantly higher proportion of underlying ischemic heart disease, graft-versus-host-disease, hypogammaglobulinemia, and concomitant pulmonary infections. There were no significant differences in mortality rates or readmission rates between the two groups. The estimated odds ratio for death in patients receiving palivizumab after adjusting for propensity scores and covariates were 0.12 ([0.01, 1.32], p = .08) and 0.09 ([0.01, 1.03], p = .05) respectively. After adjustment for factors associated with severity of illness, there was no difference in mortality among patients treated with palivizumab.
A role for &bgr;,&bgr;-xanthophylls in Arabidopsis UV-B photoprotection

Plastidial isoprenoids, such as carotenoids and tocopherols, are important anti-oxidant metabolites synthesized in plastids from precursors generated by the methylerythritol 4-phosphate (MEP) pathway. In this study, we found that irradiation of Arabidopsis thaliana plants with UV-B caused a strong increase in the accumulation of the photoprotective xanthophyll zeaxanthin but also resulted in slightly higher levels of γ-tocopherol. Plants deficient in the MEP enzymes 1-deoxy-D-xylulose 5-phosphate synthase and 1-hydroxy-2-methyl-2-butenyl 4-diphosphate synthase showed a general reduction in both carotenoids and tocopherols and this was associated with increased DNA damage and decreased photosynthesis after exposure to UV-B. Genetic blockage of tocopherol biosynthesis did not affect DNA damage accumulation. In contrast, lut2 mutants that accumulate β,β-xanthophylls showed decreased DNA damage when irradiated with UV-B. Analysis of aba2 mutants showed that UV-B protection was not mediated by ABA (a hormone derived from β,β-xanthophylls). Plants accumulating β,β-xanthophylls also showed decreased oxidative damage and increased expression of DNA-repair enzymes, suggesting that this may be a mechanism for these plants to decrease DNA damage. In addition, in vitro experiments also provided evidence that β,β-xanthophylls can directly protect against DNA damage by absorbing radiation. Together, our results suggest that xanthophyll-cycle carotenoids that protect against excess illumination may also contribute to protection against UV-B.
IL‐10(‐592A/C) gene variant a predictor of postoperative atrial fibrillation in the north Indian population

There is an accumulating body of evidence indicating a strong association between inflammation and the pathogenesis of atrial fibrillation (AF) in different ethnicities across the globe. AF increases the risk of stroke and heart failure. Despite various researches on IL‐10 response, there is limited clinical evidence present, which demonstrate a role of these immunity regulators in AF. Therefore, this study was designed to decipher the role of IL‐10(‐592A/C) polymorphism in the development of postoperative AF (post‐OP AF).
The clinical, immunological and microbiological impact of the 10-valent pneumococcal-Protein D conjugate vaccine in children with recurrent protracted bacterial bronchitis, chronic suppurative lung disease and bronchiectasis: A multi-centre, double-blind, randomised controlled trial

ABSTRACT We aimed to determine the efficacy of the 10-valent pneumococcal-Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) in children aged 18-months to <18-years with recurrent protracted bacterial bronchitis (rPBB), chronic suppurative lung disease (CSLD) or bronchiectasis. In a multi-centre, double-blind randomised controlled trial, children received two doses, 2-months apart of the 10vPHiD-CV or quadrivalent meningococcal-ACYW135 conjugate vaccine. Active surveillance for acute exacerbations, respiratory symptoms and antibiotic use was undertaken through to 12-months after the second vaccine dose (clinical cohort only). Serum, saliva and nasopharyngeal swabs were collected to measure immunological and microbiological effects (immunology cohort). Between December 2012 and August 2015, 62 children were enrolled onto the clinical protocol (1 excluded from clinical analyses due to unblinding), while 74 contributed to the immunology cohort (overall mean age = 6.8-years (standard deviation = 3.7), 42 (56.8%) male). The absolute risk difference comparing the 10vPHiD-CV group (n = 31 children) to the MenACYW135 group (n = 30 children) for acute exacerbations was -0.5 exacerbations/100-weeks at risk (95% confidence interval (CI) -2.0, 0.9). Compared to the MenACYW135 group, children who received the 10vPHiD-CV were less likely to have respiratory symptoms in each fortnight of surveillance (incidence density ratio (IDR) 0.82, 95%CI 0.61, 1.10) and required fewer short-course (<14-days duration) antibiotics (IDR 0.81, 95% CI 0.61, 1.09). The vaccine was immunogenic and no serious adverse events related to the vaccine were reported. In conclusion, 10vPHiD-CV might have a future role in managing children with rPBB, CSLD and bronchiectasis, but larger multicentre trials are needed to confirm or refute findings from this preliminary study.
The Communication Cost of Information Spreading in Dynamic Networks

This paper investigates the message complexity of distributed information spreading in adversarial dynamic networks. While distributed computations in dynamic networks have been studied intensively over the last years, almost all of the existing work solely focuses on the time complexity of distributed algorithms. In information spreading, the goal is to spread k tokens of information to every node on an n-node network. We consider the amortized (average) message complexity of spreading a token, assuming that the number of tokens is large. In a static network, this basic problem can be solved using (asymptotically optimal) O(n) amortized messages per token. Our focus is on token-forwarding algorithms, which do not manipulate tokens in any way other than storing, copying, and forwarding them. We present two sets of results depending on how nodes send messages to their neighbors: 1. Local broadcast: We show a tight lower bound of Ω(n^2) on the number of amortized local broadcasts, which is matched by the naive flooding algorithm. The lower bound holds for randomized algorithms against a strongly adaptive adversary. 2. Unicast: We study the message complexity as a function of the number of dynamic changes in the network. To facilitate this, we introduce adversary-competitive message complexity as a natural complexity measure for analyzing dynamic networks: The adversary pays a unit cost for every topological change and the message cost of an algorithm is determined as the actual number of messages sent minus the total cost of the adversary. Under this model, we give a deterministic algorithm that obtains an optimal amortized message complexity of O(n) if the number of tokens k is sufficiently large. We also present a randomized algorithm that achieves subquadratic amortized message complexity for much smaller k under an oblivious adversary.
A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding

Abstract The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
In Vitro Study of Bacteriophage AB3 Endolysin LysAB3 Activity Against Acinetobacter baumannii Biofilm and Biofilm-Bound A. baumannii.

BACKGROUND The increase in the prevalence of drug-resistant Acinetobacter baumannii is a serious public health concern, which is closely linked to the formation of biofilm. It is reported that the bacteriophage and its endolysin have a good ability to degrade biofilms. The goals of this study were to compare the ability of A. baumannii bacteriophage AB3, its endolysin AB3, and three antibiotics to degrade A. baumannii biofilm and biofilm-bound A. baumannii and to understand the antibacterial mechanism of LysAB3. METHODS The 558-bp sequence of the LysAB3 gene was amplified by polymerase chain reaction (PCR); the fragment was cloned into pET28a (+) to construct the recombinant plasmid pET28a-LysAB3, which was then expressed in E. coli BL21 (DE3) to obtain the LysAB3. Differences in A. baumannii biofilm and biofilm-bound A. baumannii after treatment with bacteriophage AB3, LysAB3 or three antibiotics were examined using the crystal violet staining method and an MTT (3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide) assay. Changes in biofilm morphology and thickness in each treatment group were observed by laser scanning confocal microscopy. In addition, a LysAB3 construct with the amphiphilic peptide structural region removed (LysAB3-D) was assessed for its antibacterial activity. RESULTS After 24-hour treatment with either bacteriophage AB3 and its LysAB3, A. baumannii biofilms were significantly degraded, and the number of viable biofilm-bound A. baumannii were also significantly decreased. After removing the amphiphilic peptide structure motif from LysAB3, the antibacterial activity decreased from 95.8% to 33.3%. CONCLUSIONS Thus, LysAB3 can effectively degrade A. baumannii biofilm and biofilm-bound A. baumannii in vitro. The antibacterial mechanism of LysAB3 may be associated with the ability of the amphiphilic peptide structural region to enhance the permeability of cytoplasmic membrane of A. baumannii by degradation of bacterial wall peptidoglycan.
Uncovering the digital “ x ” phenomena in the IS field : A text analysis approach

As digital computers permeate an increasing number of activities, the term digital is associated with more processes, entities, and objects (e.g., digital economy, digital natives). This trend reflects in Information Systems research, with “digital” appearing before existing research concepts (e.g., digital infrastructure), often substituting for “IT”. In this study, we contribute to the delineation between digital “x” and IT “x” research by investigating the degree of usage of the terms and uncovering the most widespread digital “x” constructs. Using text analysis techniques, we can analyze a broad set of journals and a long time period. Early results, based on 17 years of MIS Quarterly publications, confirm the increasing use of the term digital. Conversely, digitize and digitalize, the two main forms of the term digital, are rarely used and do not show any significant increase in usage over time. While preliminary and not concluding, our results confirm the increasing popularity of the term digital. However, a limited number of digital “x” terms appear to connote novel constructs and the bulk of the research does not address the socio-technical process of digitalization that is central to the IS discipline. We discuss the implications of our early results and provide a research agenda.
Short-course High-dose Liposomal Amphotericin B for Human Immunodeficiency Virus–associated Cryptococcal Meningitis: A Phase 2 Randomized Controlled Trial

Background We performed a phase 2 noninferiority trial examining the early fungicidal activity (EFA) of 3 short-course, high-dose liposomal amphotericin B (L-AmB) regimens for cryptococcal meningitis (CM) in Tanzania and Botswana. Methods Human immunodeficiency virus (HIV)-infected adults with CM were randomized to (i) L-AmB 10 mg/kg on day 1 (single dose); (ii) L-AmB 10 mg/kg on day 1 and 5 mg/kg on day 3 (2 doses); (iii) L-AmB 10 mg/kg on day 1 and 5 mg/kg on days 3 and 7 (3 doses); or (iv) L-AmB 3 mg/kg/day for 14 days (control). All patients also received oral fluconazole 1200 mg/day for 14 days. Primary endpoint was mean rate of clearance of cerebrospinal fluid cryptococcal infection (EFA). Noninferiority was defined as an upper limit of the 2-sided 95% confidence interval (CI) of difference in EFA between intervention and control <0.2 log10 colony-forming units (CFU)/mL/day. Results Eighty participants were enrolled. EFA for daily L-AmB was -0.41 log10 CFU/mL/day (standard deviation, 0.11; n = 17). Difference in mean EFA from control was -0.11 (95% CI, -.29 to .07) log10 CFU/mL/day faster with single dose (n = 16); -0.05 (95% CI, -.20 to .10) log10 CFU/mL/day faster with 2 doses (n = 18); and -0.13 (95% CI, -.35 to .09) log10 CFU/mL/day faster with 3 doses (n = 18). EFA in all short-course arms was noninferior to control. Ten-week mortality was 29% (n = 23) with no statistical difference between arms. All arms were well tolerated. Conclusions Single-dose 10 mg/kg L-AmB was well tolerated and led to noninferior EFA compared to 14 days of 3 mg/kg/day L-AmB in HIV-associated CM. Induction based on a single 10 mg/kg L-AmB dose is being taken forward to a phase 3 clinical endpoint trial. Clinical Trials Registration ISRCTN 10248064.
A Practical Incremental Learning Framework For Sparse Entity Extraction

This work addresses challenges arising from extracting entities from textual data, including the high cost of data annotation, model accuracy, selecting appropriate evaluation criteria, and the overall quality of annotation. We present a framework that integrates Entity Set Expansion (ESE) and Active Learning (AL) to reduce the annotation cost of sparse data and provide an online evaluation method as feedback. This incremental and interactive learning framework allows for rapid annotation and subsequent extraction of sparse data while maintaining high accuracy. We evaluate our framework on three publicly available datasets and show that it drastically reduces the cost of sparse entity annotation by an average of 85% and 45% to reach 0.9 and 1.0 F-Scores respectively. Moreover, the method exhibited robust performance across all datasets.
Analytical Estimation of Reactive Power Capability of a Radial Distribution System

The control of reactive power exchange between grids of different voltage levels has always been a concern for system operators. With production moving from the transmission to the distribution level, its importance increases. This paper proposes a novel approach to estimate reactive power capability of the grid as a whole. A linearized analytical model for an estimation of available reactive power exchange at the interface between two grids has been developed. The maximum estimation error for the scenarios we tested was only 2%. The model gives the relation between important grid parameters and the supported reactive power. The conclusions drawn from the model are confirmed on typical Swedish distribution network with scattered wind power and small industry consumers. Common scenarios in development of distribution grids are applied to show relevant parameters influence. One studied scenario is replacement of overhead lines with cables. It is shown that this particular change enhances the reactive power capability of the grid which is directly seen from the analytical analysis without running any optimal power flow. The analytical model proposed in this paper gives fundamental understanding of the reactive power capability of radial distribution grids.
Defective and clustered choosability of sparse graphs

Abstract An (improper) graph colouring has defect d if each monochromatic subgraph has maximum degree at most d, and has clustering c if each monochromatic component has at most c vertices. This paper studies defective and clustered list-colourings for graphs with given maximum average degree. We prove that every graph with maximum average degree less than (2d+2)/(d+2)k is k-choosable with defect d. This improves upon a similar result by Havet and Sereni (J. Graph Theory, 2006). For clustered choosability of graphs with maximum average degree m, no (1-ɛ)m bound on the number of colours was previously known. The above result with d=1 solves this problem. It implies that every graph with maximum average degree m is $\lfloor{\frac{3}{4}m+1}\rfloor$-choosable with clustering 2. This extends a result of Kopreski and Yu (Discrete Math., 2017) to the setting of choosability. We then prove two results about clustered choosability that explore the trade-off between the number of colours and the clustering. In particular, we prove that every graph with maximum average degree m is $\lfloor{\frac{7}{10}m+1}\rfloor$-choosable with clustering 9, and is $\lfloor{\frac{2}{3}m+1}\rfloor$-choosable with clustering O(m). As an example, the later result implies that every biplanar graph is 8-choosable with bounded clustering. This is the best known result for the clustered version of the earth–moon problem. The results extend to the setting where we only consider the maximum average degree of subgraphs with at least some number of vertices. Several applications are presented.