bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Medically Important Yeasts Using PCR-Based Detection of DNA Sequence Polymorphisms in the Internal Transcribed Spacer 2 Region of the rRNA Genes
Authors: Chen Y. C. , Eisner J. D. , Kattar M. M. , Rassoulian-Barrett S. L. , LaFe K. , Yarfitz S. L. , Limaye A. P. , Cookson B. T.
Published: March 2020

Identification of medically relevant yeasts can be time-consuming and inaccurate with current methods. We evaluated PCR-based detection of sequence polymorphisms in the internal transcribed spacer 2 (ITS2) region of the rRNA genes as a means of fungal identification. Clinical isolates (401), reference strains (6), and type strains (27), representing 34 species of yeasts were examined. The length of PCR-amplified ITS2 region DNA was determined with single-base precision in less than 30 min by using automated capillary electrophoresis. Unique, species-specific PCR products ranging from 237 to 429 bp were obtained from 92% of the clinical isolates. The remaining 8%, divided into groups with ITS2 regions which differed by ≤2 bp in mean length, all contained species-specific DNA sequences easily distinguishable by restriction enzyme analysis. These data, and the specificity of length polymorphisms for identifying yeasts, were confirmed by DNA sequence analysis of the ITS2 region from 93 isolates. Phenotypic and ITS2-based identification was concordant for 427 of 434 yeast isolates examined using sequence identity of ≥99%. Seven clinical isolates contained ITS2 sequences that did not agree with their phenotypic identification, and ITS2-based phylogenetic analyses indicate the possibility of new or clinically unusual species in the
Rhodotorula
and
Candida
genera. This work establishes an initial database, validated with over 400 clinical isolates, of ITS2 length and sequence polymorphisms for 34 species of yeasts. We conclude that size and restriction analysis of PCR-amplified ITS2 region DNA is a rapid and reliable method to identify clinically significant yeasts, including potentially new or emerging pathogenic species.
Multicenter Evaluation of Methods To Quantitate Human Immunodeficiency Virus Type 1 RNA in Seminal Plasma
Authors: Fiscus Susan A. , Brambilla Don , Coombs Robert W. , Yen-Lieberman Belinda , Bremer James , Kovacs Andrea , Rasheed Suraiya , Vahey Maryanne , Schutzbank Ted , Reichelderfer Patricia S. , Group other members of the Aids Clinical Trials Group Genital Secr
Published: March 2020

We have evaluated two commercially available kits (AMPLICOR MONITOR [Roche] and NASBA HIV-1 QT or NucliSens HIV-1 QT [Organon Teknika]) and two noncommercial methods for the accurate quantitation of human immunodeficiency virus type 1 (HIV-1) RNA in seminal plasma. The same panels of coded specimens were tested on four separate occasions. Laboratories using the commercial assays employed silica beads to isolate HIV-1 RNA, which removed inhibitory factors sometimes found in seminal plasma. Sensitivities and specificities, respectively, for each assay were as follows: AMPLICOR MONITOR, 100 and 73%; NASBA HIV-1 QT, 84 and 100%; NucliSens HIV-1 QT, 99 and 98%; and noncommercial assays, 91 and 73%. When results from the laboratory that was inexperienced with the silica bead extraction method were excluded from the analysis, specificity for the Roche assay increased to 100%. The commercial assays demonstrated highly reproducible results, with intra-assay standard deviations (measured in log
10
RNA copies/milliliter of seminal plasma) ranging from 0.11 to 0.32; those of the noncommercial assays ranged from 0.12 to 0.75. Differences in mean estimated HIV-1 RNA concentrations were ≤0.67 log
10
and were greater at low viral loads. Suspension matrices that used blood plasma or seminal plasma did not make a difference in recovery of HIV-1 RNA, which suggested that blood plasma specimens can be used as external controls for seminal plasma assays. More variation in the HIV-1 RNA viral loads was observed in the seminal plasma values than in the blood plasma values when paired specimens from HIV-1-infected men were tested. Quantitation of HIV-1 RNA in seminal plasma can be reliably accomplished using two commercially available assays, and may be incorporated into the evaluations of HIV-1 seropositive men enrolled in clinical studies.
Genetic Homology among Thirteen
Encephalitozoon intestinalis
Isolates Obtained from Human Immunodeficiency Virus-Infected Patients with Intestinal Microsporidiosis
Authors: Liguory Olivier , Fournier Sandra , Sarfati Claudine , Derouin Francis , Molina Jean-Michel
Published: March 2020

The ribosomal DNA internal transcribed spacer sequences of 13 unrelated
Encephalitozoon intestinalis
isolates obtained from human immunodeficiency virus (HIV)-infected patients with intestinal microsporidiosis were analyzed by gene amplification and DNA sequencing. Among these isolates, we found only one genetic lineage which suggests that
E. intestinalis
may have a clonal distribution in HIV-infected patients.
Molecular Characterization of Porcine Rotaviruses from the Southern Region of Brazil: Characterization of an Atypical Genotype G[9] Strain
Authors: Rácz Maria Lucia , Kroeff Suzana S. , Munford Veridiana , Caruzo Thabata A. R. , Durigon Edison L. , Hayashi Yasuyoshi , Gouvea Vera , Palombo Enzo A.
Published: March 2020

The G (VP7) and P (VP4) serotype distribution of Brazilian porcine rotaviruses was determined using reverse transcription-PCR genotyping methods. Common porcine G types G3, G4, and G5 were detected in combination with P types [6] and [7]. The detection of nonporcine G types and unusual G-P combinations and the characterization of an atypical virus indicated that interspecies transmission may contribute to the genetic diversity of porcine rotaviruses.
Species-Specific Recognition of
Sulfolobales
Mediated by UV-Inducible Pili and S-Layer Glycosylation Patterns
Authors: van Wolferen Marleen , Shajahan Asif , Heinrich Kristina , Brenzinger Susanne , Black Ian M. , Wagner Alexander , Briegel Ariane , Azadi Parastoo , Albers Sonja-Verena
Published: March 2020

Type IV pili can be found on the cell surface of many archaea and bacteria where they play important roles in different processes. The UV-inducible pili system of
Sulfolobales
(Ups) pili from the crenarchaeal
Sulfolobales
species are essential in establishing species-specific mating partners, thereby assisting in genome stability. With this work, we show that different
Sulfolobus
species have specific regions in their Ups pili subunits, which allow them to interact only with cells from the same species. Additionally, different
Sulfolobus
species have unique surface-layer
N-
glycosylation patterns. We propose that the unique features of each species allow the recognition of specific mating partners. This knowledge for the first time gives insights into the molecular basis of archaeal self-recognition.
Cyclic di-GMP Signaling in Bacillus subtilis Is Governed by Direct Interactions of Diguanylate Cyclases and Cognate Receptors
Authors: Kunz Sandra , Tribensky Anke , Steinchen Wieland , Oviedo-Bocanegra Luis , Bedrunka Patricia , Graumann Peter L.
Published: March 2020

Second messengers are free to diffuse through the cells and to activate all responsive elements. Cyclic di-GMP (c-di-GMP) signaling plays an important role in the determination of the life style transition between motility and sessility/biofilm formation but involves numerous distinct synthetases (diguanylate cyclases [DGCs]) or receptor pathways that appear to act in an independent manner. Using
Bacillus subtilis
as a model organism, we show that for two c-di-GMP pathways, DGCs and receptor molecules operate via direct interactions, where a synthesized dinucleotide appears to be directly used for the protein-protein interaction. We show that very few DGC molecules exist within cells; in the case of exopolysaccharide (EPS) formation via membrane protein DgcK, the DGC molecules act at a single site, setting up a single signaling pool within the cell membrane. Using single-molecule tracking, we show that the soluble DGC DgcP arrests at the cell membrane, interacting with its receptor, DgrA, which slows down motility. DgrA also directly binds to DgcK, showing that divergent as well as convergent modules exist in
B. subtilis
. Thus, local-pool signal transduction operates extremely efficiently and specifically.
The Absence of (p)ppGpp Renders Initiation of Escherichia coli Chromosomal DNA Synthesis Independent of Growth Rates
Authors: Fernández-Coll Llorenç , Maciag-Dorszynska Monika , Tailor Krishma , Vadia Stephen , Levin Petra Anne , Szalewska-Palasz Agnieszka , Cashel Michael
Published: March 2020

Bacterial cells regulate their own chromosomal DNA synthesis and cell division depending on the growth conditions, producing more DNA when growing in nutritionally rich media than in poor media (i.e., human gut versus water reservoir). The accumulation of the nucleotide analog (p)ppGpp is usually viewed as serving to warn cells of impending peril due to otherwise lethal sources of stress, which stops growth and inhibits DNA, RNA, and protein synthesis. This work importantly finds that small physiological changes in (p)ppGpp basal levels associated with slow balanced exponential growth incrementally inhibit the intricate process of initiation of chromosomal DNA synthesis. Without (p)ppGpp, initiations mimic the high rates present during fast growth. Here, we report that the effect of (p)ppGpp may be due to the regulation of the expression of gyrase, an important enzyme for the replication of DNA that is a current target of several antibiotics.
Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a
ridA
Mutant of Salmonella enterica
Authors: Borchert Andrew J. , Gouveia Goncalo J. , Edison Arthur S. , Downs Diana M.
Published: March 2020

The accumulation of the reactive enamine intermediate 2-aminoacrylate (2AA) elicits global metabolic stress in many prokaryotes and eukaryotes by simultaneously damaging multiple pyridoxal 5′-phosphate (PLP)-dependent enzymes. This work employed
1
H NMR to expand our understanding of the consequence(s) of 2AA stress on metabolite pools and effectively identify the metabolic changes stemming from one damaged target: GlyA. This study shows that nutrient supplementation during
1
H NMR metabolomics experiments can disentangle complex metabolic outcomes stemming from a general metabolic stress. Metabolomics shows great potential to complement classical reductionist approaches to cost-effectively accelerate the rate of progress in expanding our global understanding of metabolic network structure and physiology. To that end, this work demonstrates the utility in implementing nutrient supplementation and genetic perturbation into metabolomics workflows as a means to connect metabolic outputs to physiological phenomena and establish causal relationships.
Phenotype and variations associated with the deletion of the 1q44 cytoband and the pathogenic duplication in the 9q32q34.3 cytobands
Authors: Gómez-Carpintero García Ana , Vidal Esteban Ana , Bermejo Gómez Amanda , Púa Torrejón Ruth Camila
Published: March 2020

​The advance in the human genetic field has permitted to identify small chromosome alterations and associate them to a specific phenotype. However, there are many mutations that have not yet been described in the literature. We describe the clinical case of a term newborn with appropriate weight to its gestational age, without perinatal background of interest that, at birth, presented: macrocephaly, hypertelorism, low-set ears, prominent forehead, micrognathia, camptodactyly, bilateral cryptorchidism, inspiratory stridor with the cry, multifocal systolic murmur, wide anterior fontanel and hypotonia of mixed characteristics and in whom a deletion of the 1q44 cytoband and a pathogenic duplication in the 9q32q34.3 cytoband were detected. We perform a review of the literature.
Sex-specific and age-specific suicide mortality by method in 58 countries between 2000 and 2015
Authors: Wu Yue , Schwebel David C , Huang Yun , Ning Peishan , Cheng Peixia , Hu Guoqing
Published: March 2020

Objective

To examine recent changes in sex-specific and age-specific suicide mortality by method across countries.

Methods

Using mortality data from the WHO mortality database, we compared sex-specific, age-specific and country-specific suicide mortality by method between 2000 and 2015. We considered seven major suicide methods: poisoning by pesticides, all other poisoning, firearms and explosives, hanging, jumping from height, drowning and other methods. Changes in suicide mortality were quantified using negative binomial models among three age groups (15–44 years, 45–64 years, and 65 years and above) for males and females separately.

Results

Suicide mortality declined substantially for both sexes and all three age groups studied in 37 of the 58 included countries between 2000 and 2015. Males consistently had much higher suicide mortality rates than females in all 58 countries. Hanging was the most common suicide method in the majority of 58 countries. Sex-specific suicide mortality varied across 58 countries significantly for all three age groups. The spectrum of suicide method generally remained stable for 28 of 58 included countries; notable changes occurred in the other 30 countries, including especially Colombia, Finland and Trinidad and Tobago.

Conclusion

Likely as a result of prevention efforts as well as sociodemographic changes, suicide mortality decreased substantially in 37 of the included 58 countries between 2000 and 2015. Further actions are needed to explore specific drivers of the recent changes (particularly for increases in eight countries), to understand substantial disparities in suicide rates across countries, and to develop interventions to reduce suicide rates globally.
Head-to-head comparison of in-house produced CD19 CAR-T cell in ALL and NHL patients
Authors: Itzhaki Orit , Jacoby Elad , Nissani Abraham , Levi Michal , Nagler Arnon , Kubi Adva , Brezinger Karin , Brayer Hadar , Zeltzer Li-at , Rozenbaum Meir , Vernitsky Helly , Markel Gal , Toren Amos , Avigdor Abraham , Schachter Jacob , Besser Michal J
Published: March 2020

Background

CD19 chimeric antigen receptor T (CAR-T) cells demonstrate remarkable remission rates in pediatric and adult patients with refractory or relapsed (r/r) acute lymphoblastic leukemia (ALL) and non-Hodgkin's lymphoma (NHL). In 2016, we initiated a clinical trial with in-house produced CD19 CAR-T cells with a CD28 co-stimulatory domain. We analyzed, for the first time, differences in production features and phenotype between ALL and NHL patients.

Methods

Non-cryopreserved CAR-T cells were produced from patients’ peripheral blood mononuclear cells within 9 to 10 days. 93 patients with r/r ALL and NHL were enrolled under the same study. CAR-T cells of ALL and NHL patients were produced simultaneously, allowing the head-to-head comparison.

Results

All patients were heavily pretreated. Three patients dropped out from the study due to clinical deterioration (n=2) or production failure (n=1). Cells of ALL patients (n=37) expanded significantly better and contained more CAR-T cells than of NHL patients (n=53). Young age had a positive impact on the proliferation capacity. The infusion products from ALL patients contained significantly more naïve CAR-T cells and a significantly higher expression of the chemokine receptor CXCR3. PD-1, LAG-3, TIM-3, and CD28 were equally expressed. 100% of ALL patients and 94% of NHL patients received the target dose of 1×10e6 CAR-T/kg. The overall response rate was 84% (30/36) in ALL and 62% (32/52) in NHL. We further compared CAR-T cell infusion products to tumor infiltrating lymphocytes (TIL), another common type of T cell therapy, mainly clinically effective in solid tumors. CAR-T cells contained significantly more naïve T cells and central memory T cells and significantly less CCR5 compared to TIL infusion products.

Conclusions

The in-house production of CAR-T cells is highly efficient and fast. Clinical response rate is high. CAR-T cells can be successfully produced for 99% of patients in just 9 to 10 days. Cells derived from ALL patients demonstrate a higher proliferation rate and contain higher frequencies of CAR-T cells and naïve T cells than of NHL patients. In addition, understanding the differences between CAR-T and TIL infusion products, may provide an angle to develop CAR-T cells for the treatment of solid tumors in the future.

Trial registration number

ClinicalTrials.gov; CAR-T:NCT02772198, First posted: May 13, 2016; TIL:NCT00287131, First posted: February 6, 2006.
Enhancing fatigue resistance of activated tungsten inert gas welded UNS S32750 super duplex stainless steel by optimizing its technological properties
Authors: Arunmani A. , Senthilkumar T.
Published: March 2020

In engineering industries and heavy manufacturing plants, fatigue life of joints plays a pivotal role in determining the overall life span of the welded joint. In this paper, an advanced fusion joining technique, namely activated tungsten inert gas welding, was used for joining UNS S32750 super duplex stainless steel, with ZnO as activation flux. For the enhancement of fatigue resistance of joints, important welding process parameters were fluctuated according to a developed central composite design model. Empirical relationships were developed between the process parameters and the fatigue strength of the joints, which was correlated with the number of cycles to failure (NCF). Using analysis of variance, the significance of the developed fatigue model was ascertained. Using response surface methodology, optimization of process parameters for enhancement of fatigue resistance was done. It was observed that at the optimized activated tungsten inert gas weld process parameters of travel speed of welding torch at 69.85 mm/min, weld current at 125.20 A, and shielding gas flow rate at 14.77 L/min, a high fatigue life of 7.66396 × 108 NCF was obtained and the model was validated to very high predictability. Microstructural variations in the fatigue-tested specimens were evaluated for identifying the grain modifications.
Constrained k-Center Problem on a Convex Polygon
Authors: Basappa Manjanna , Jallu Ramesh K. , Das Gautam K.
Published: March 2020

In this paper, we consider a restricted covering problem, in which a convex polygon [Formula: see text] with [Formula: see text] vertices and an integer [Formula: see text] are given, the objective is to cover the entire region of [Formula: see text] using [Formula: see text] congruent disks of minimum radius [Formula: see text], centered on the boundary of [Formula: see text]. For [Formula: see text] and any [Formula: see text], we propose an [Formula: see text]-factor approximation algorithm for this problem, which runs in [Formula: see text] time. The best known approximation factor of the algorithm for the problem in the literature is 1.8841 [H. Du and Y. Xu: An approximation algorithm for [Formula: see text]-center problem on a convex polygon, J. Comb. Optim. 27(3) (2014) 504–518].
A Cohen-type theorem for w-Artinian modules
Authors: Zhou Dechuan , Kim Hwankoo , Hu Kui
Published: March 2020

Let [Formula: see text] be a commutative ring with identity. In this paper, a Cohen-type theorem for [Formula: see text]-Artinian modules is given, i.e. a [Formula: see text]-cofinitely generated [Formula: see text]-module [Formula: see text] is [Formula: see text]-Artinian if and only if [Formula: see text] is [Formula: see text]-cofinitely generated for every prime [Formula: see text]-ideal [Formula: see text] of [Formula: see text]. As a by-product of the proof, we also obtain a detailed representation of elements of a [Formula: see text]-module and the [Formula: see text]-theoretic version of the Chinese remainder theorem for both modules and rings.
Computational study of reverse water gas shift reaction on Cu38 cluster model and Cu slab model
Authors: Qi Dabin , Luo Xudong , Yao Jun , Lu Xiaojun , Zhang Zhan
Published: March 2020

Density functional theory (DFT) calculation has been applied to investigate the adsorption behaviors of reactive adsorbate and the reaction pathway of reverse water gas shift (RWGS) reaction on Cu[Formula: see text] cluster and Cu slab surface. The possible adsorption configuration, sites and energies of reactive intermediates on Cu[Formula: see text] cluster and Cu slab surface have been calculated to reveal the effects between Cu[Formula: see text] cluster and Cu slab surface. In addition, transition states, reaction energies and activation barriers were calculated to RWGS mechanism on Cu[Formula: see text] cluster and Cu slab model. Compared to the mechanism of RWGS on different surfaces, it was found the Cu[Formula: see text] cluster facilitates the RWGS reaction. The intrinsic differences between Cu cluster and Cu slab model suggest that surface defects play a pivotal role in RWGS reaction.
Computational design of an intramolecular frustrated lewis pair catalyst for enantioselective hydrogenation
Authors: Sharma Gitanjali , Newman Paul D. , Melen Rebecca , Platts James A.
Published: March 2020

We report DFT calculations on potential intramolecular, enantioselective hydrogenation catalysts based around borenium-carbenes based on a camphor scaffold. Using the M06-2X meta-hybrid functional, we find frustrated Lewis pair (FLP) behavior with suitably chosen linkers that prevent association of Lewis bases with the borenium center. These intramolecular FLPs are predicted to be able to heterolytically dissociate H2. Barriers to dissociation and the endo/exoergic nature of the reaction can be tuned by the nature of the base and substituent on B. The reactivity of the hydrogenated FLP catalyst with olefin and carbonyl substrates is then explored: we predict concerted reactions for all substrates considered with relatively low barriers and large exoergic character. Hydrogenation of both faces of a prochiral substrate is also examined, indicating a small but significant variation in reaction barrier in favor of the Si-face, ascribed to stronger interactions with the aromatic [Formula: see text]-system in the TS compared to the Re-face.
Optimization Methods for Redundancy Allocation in Large Systems
Authors: Leon Florin , Caşcaval Petru , Bădică Costin
Published: March 2020

This paper addresses the issue of optimal allocation of spare modules in large series-redundant systems in order to obtain a required reliability under cost constraints. Both cases of active and standby redundancy are considered. Moreover, for a subsystem with standby redundancy, two cases are examined: in the first case, all the spares are maintained in cold state (cold standby redundancy) and, in the second one, to reduce the time needed to put a spare into operation when the active one fails, one of the spares is maintained in warm conditions. To solve this optimization problem, for the simpler case of active redundancy an analytical method based on the Lagrange multipliers technique is first applied. Then the results are improved by using Pairwise Hill Climbing, an original fine-tuning algorithm. An alternative approach is an innovative evolutionary algorithm, RELIVE, in which an individual lives for several generations and improves its fitness based on local search. These methods are especially needed in case of very large systems.
Deep-water sand-fairway mapping as a tool for tectonic restoration: decoding Miocene central Mediterranean palaeogeography using the Numidian turbidites of southern Italy
Authors: Butler Robert W.H. , Pinter Patricia R. , Maniscalco Rosanna , Hartley Adrian J.
Published: March 2020

As turbidity currents are sensitive to the geometry of the substrate across which they flow, the sedimentology of turbidites can chart the development of submarine structures and reveal regional palaeobathymetric connections. This rationale is applied to understand the tectonic evolution of the central Mediterranean in the early Miocene, using the African-sourced, hyper-mature Numidian sandstones and their immature, orogen-derived time-equivalents. In both Sicily and the southern Apennines, the Numidian sequence displays characteristics of confined–uncontained turbidites: grain-size breaks and coarse bedload indicative of ubiquitous flow bypass; short-range grain-size fractionation across flow; stacked sandy bed-sets in the flow axes. We reconstruct sand fairways for over 300 km across the region and propose that their causative flows, axially fed from north Africa, were confined along sinuous corridors created by active submarine thrusting. In contrast, orogen-derived turbidites (e.g. Reitano flysch, confined–contained turbidites) were ponded in mini-basins higher on the thrust wedge. The composite Apennine–Calabrian–Maghrebian orogen with its submarine thrust belt had occluded deep-water Tethyan connections through the central Mediterranean by early Miocene times. Palaeobathymetry across the submarine thrust belt increased northwards into the future Apennines. This study illustrates the utility of turbidite sedimentology, especially reconstructing sand fairways, in building palaeogeographical reconstructions of complex tectonic regimes.
Submatrix Maximum Queries in Monge and Partial Monge Matrices Are Equivalent to Predecessor Search
Authors: Gawrychowski Paweł , Mozes Shay , Weimann Oren
Published: March 2020

We present an optimal data structure for submatrix maximum queries in
n
×
n
Monge matrices. Our result is a two-way reduction showing that the problem is equivalent to the classical predecessor problem in a universe of polynomial size. This gives a data structure of
O
(
n
) space that answers submatrix maximum queries in
O
(log log
n
) time, as well as a matching lower bound, showing that
O
(log log
n
) query-time is optimal for any data structure of size
O
(
n
polylog(
n
)). Our result settles the problem, improving on the
O
(log
2
n
) query time in SODA’12, and on the
O
(log
n
) query-time in ICALP’14.

In addition, we show that partial Monge matrices can be handled in the same bounds as full Monge matrices. In both previous results, partial Monge matrices incurred additional inverse-Ackermann factors.
Doubly Balanced Connected Graph Partitioning
Authors: Soltan Saleh , Yannakakis Mihalis , Zussman Gil
Published: March 2020

We introduce and study the doubly balanced connected graph partitioning problem: Let
G
=(
V
,
E
) be a connected graph with a weight (supply/demand) function
p
:
V
→ {−1, +1} satisfying
p
(
V
)=∑

j
&isin
V
p

(
j
) = 0. The objective is to partition
G
into (
V
1
,
V
2
) such that
G
[
V
1
] and
G
[
V
2
] are connected, ∣
p
(
V
1
)∣,∣
p
(
V
2
)∣≤
c

p

, and max{ ∣
V
1
/
V
2
∣,∣
V
2
/
V
1
∣} ≤
c

s

, for some constants
c

p

and
c

s

. When
G
is 2-connected, we show that a solution with
c

p

=1 and
c

s

=2 always exists and can be found in randomized polynomial time. Moreover, when
G
is 3-connected, we show that there is always a “perfect” solution (a partition with
p
(
V
1
)=
p
(
V
2
)=0 and ∣
V
1
∣=∣
V
2
∣, if ∣
V
∣≡ 0 (mod 4)), and it can be found in randomized polynomial time. Our techniques can be extended, with similar results, to the case in which the weights are arbitrary (not necessarily ±1), and to the case that
p
(
V
)≠ 0 and the excess supply/demand should be split evenly. They also apply to the problem of partitioning a graph with two types of nodes into two large connected subgraphs that preserve approximately the proportion of the two types.
Subexponential Algorithms for Rectilinear Steiner Tree and Arborescence Problems
Authors: Fomin Fedor V. , Lokshtanov Daniel , Kolay Sudeshna , Panolan Fahad , Saurabh Saket
Published: March 2020

A
rectilinear Steiner tree
for a set
K
of points in the plane is a tree that connects
k
using horizontal and vertical lines. In the R
ectilinear
S
teiner
T
ree
problem, the input is a set
K
={
z
1
,
z
2
,…,
z

n

} of
n
points in the Euclidean plane (R
2
), and the goal is to find a rectilinear Steiner tree for
k
of smallest possible total length. A
rectilinear Steiner arborescence
for a set
k
of points and a root
r
∈
K
is a rectilinear Steiner tree
T
for
K
such that the path in
T
from
r
to any point
z
∈
K
is a shortest path. In the R
ectilinear
S
teiner
A
rborescence
problem, the input is a set
K
of
n
points in R
2
, and a root
r
∈
K
, and the task is to find a rectilinear Steiner arborescence for
K
, rooted at
r
of smallest possible total length. In this article, we design deterministic algorithms for these problems that run in 2

O
(√
n
log
n
)

time.
k
-center Clustering under Perturbation Resilience
Authors: Balcan Maria-Florina , Haghtalab Nika , White Colin
Published: March 2020

The
k
-center problem is a canonical and long-studied facility location and clustering problem with many applications in both its symmetric and asymmetric forms. Both versions of the problem have tight approximation factors on worst case instances: a 2-approximation for symmetric
k
-center and an
O
(log
*
(
k
))-approximation for the asymmetric version. Therefore, to improve on these ratios, one must go beyond the worst case.

In this work, we take this approach and provide strong positive results both for the asymmetric and symmetric
k
-center problems under a natural input stability (promise) condition called
α-perturbation resilience
[15], which states that the optimal solution does not change under any α-factor perturbation to the input distances. We provide algorithms that give strong guarantees simultaneously for stable and non-stable instances: Our algorithms always inherit the worst-case guarantees of clustering approximation algorithms and output the optimal solution if the input is 2-perturbation resilient. In particular, we show that if the input is only perturbation resilient on part of the data, our algorithm will return the optimal clusters from the region of the data that is perturbation resilient while achieving the best worst-case approximation guarantee on the remainder of the data. Furthermore, we prove that our result is tight by showing symmetric
k
-center under (2 − ϵ)-perturbation resilience is hard unless
NP
=
RP
.

The impact of our results is multifaceted. First, to our knowledge, asymmetric
k
-center is the first problem that is hard to approximate to any constant factor in the worst case, yet can be optimally solved in polynomial time under perturbation resilience for a constant value of α. This is also the first tight result for any problem under perturbation resilience, i.e., this is the first time the exact value of α for which the problem switches from being NP-hard to efficiently computable has been found. Furthermore, our results illustrate a surprising relationship between symmetric and asymmetric
k
-center instances under perturbation resilience. Unlike approximation ratio, for which symmetric
k
-center is easily solved to a factor of 2 but asymmetric
k
-center cannot be approximated to any constant factor, both symmetric and asymmetric
k
-center can be solved optimally under resilience to 2-perturbations. Finally, our guarantees in the setting where only part of the data satisfies perturbation resilience make these algorithms more applicable to real-life instances.
Combinatorial Auctions Do Need Modest Interaction
Authors: Assadi Sepehr
Published: March 2020

We study the necessity of interaction for obtaining efficient allocations in combinatorial auctions with
subadditive bidders
. This problem was originally introduced by Dobzinski, Nisan, and Oren (STOC’14) as the following simple market scenario:
m
items are to be allocated among
n
bidders in a distributed setting where bidders valuations are private and hence
communication
is needed to obtain an efficient allocation. The communication happens in rounds: In each round, each bidder,
simultaneously
with others, broadcasts a message to all parties involved. At the end, the central planner computes an allocation solely based on the communicated messages. Dobzinski et al. showed that (at least some) interaction is necessary for obtaining even an approximately efficient allocation: No non-interactive (1-round) protocol with polynomial communication (in the number of items and bidders) can achieve approximation ratio better than Ω(
m
1/4
), while for any
r
≥ 1, there exists
r
-round protocols that achieve
Õ
(
r
·
m

1/(
r
+1)

) approximation with polynomial communication. This in particular implies that
O
(log
m
) rounds of interaction
suffice
to obtain an approximately efficient allocation—namely, a polylog(m)-approximation.

A natural question at this point is to identify the "right" level of interaction (i.e., number of rounds)
necessary
to obtain approximately efficient allocations. In this article, we resolve this question by providing an almost tight
round-approximation
tradeoff for this problem: We show that for any
r
≥ 1, any
r
-round protocol that uses poly(
m
,
n
) bits of communication can only approximate the social welfare up to a factor of Ω(1/
r
·
m

1/(2
r
+1)

). This in particular implies that Ω(log
m
/log log
m
) rounds of interaction are
necessary
for obtaining any allocation with a reasonable welfare approximation—namely, a constant or even a polylog(
m
)-approximation. Our work builds on the multi-party round-elimination technique of Alon, Nisan, Raz, and Weinstein (FOCS’15)—used to prove similar-in-spirit lower bounds for round-approximation tradeoff in unit-demand markets—and settles an open question posed initially by Dobzinski et al. (STOC’14) and subsequently by Alon et al. (FOCS’15).
Experimental Research and Sensitivity Analysis of Mudstone Similar Materials Based on Orthogonal Design
Authors: Wen Caoxuan , Jia Shanpo , Fu Xiaofei , Meng Lingdong , Zhao Zhenyun
Published: March 2020

Due to the strong hydration sensitivity of mudstone, drilling of deep mudstone is difficult and pricy, which results in the study on its physical and mechanical properties inseparable from similar material tests. On these bases, triaxial compression and Brazilian tensile tests of the original mudstone drilled from the caprock of the D5 aquifer structure are carried out. Then, orthogonal experiments of mudstone similar materials with river sand and barite powder as aggregate and cement and gypsum as the binder are conducted, which include 3 factors that, respectively, are mass ratio of aggregate to binder, mass ratio of cement to gypsum, and barite powder content, and each factor contains 5 levels, totalling 25 groups of 150 samples. By comparing the results of mudstone and artificial samples made of similar materials, it is obvious that artificial samples and mudstone are significantly similar in terms of density, compressive strength, elastic modulus, and compressive strength when the aggregate‐binder ratio is about 4, 8, 5, and 4, respectively. Further sensitivity analysis showed that the aggregate‐binder ratio played a major role in controlling the properties of artificial samples, while the sensitivity of different parameters to the cement‐gypsum ratio and barite content was different. The results indicate that the selected raw materials and their proportion are feasible, which can meet similar requirements and can be a reference for similar material experimental research of target mudstone.
Effect of Multistage Thermal Cracking on Permeability of Granite
Authors: Feng Zi-jun , Zhao Yang-sheng , Zhao Peng , Wan Zhi-jun
Published: March 2020

Experiments on thermal cracking in granite sample were conducted through acoustic emission monitoring, and changes in permeability were concomitantly studied using 600°C 20 MN servo‐controlled triaxial rock mechanics testing machine. Two granite samples, 200 mm in diameter and 400 mm long, from Shandong, China, were selected for these experiments. Both samples were heated up to 500°C at ambient pressure. We find that thermal cracking of large‐scaled granite is discontinuous and exhibits multiple stages with temperature. In addition, the permeability exhibits the following characteristics: (a) it neither increases nor decreases monotonously with the temperature rising and it exhibits multipeak due to the multistage thermal cracking; (b) the temperature of permeability peak lags behind that of the drastic acoustic emission activities. Both AE counts and permeability dramatically increased after 300°C, which indicated serious thermal cracking occurred after 300°C. Permeability ratio is approximately linear with the ratio of AE cumulative counts. The results will be helpful for understanding the mechanism of geothermal reservoir construction and long‐term evaluation of safety for nuclear waste geological disposal.
Observed Ground Pressure Acting on the Lining of a Large‐Diameter Shield Tunnel in Sandy Stratum under High Water Pressure
Authors: Li Xue , Zhou Shunhua , Di Honggui
Published: March 2020

Accurately evaluating the ground pressure on the tunnel lining greatly helps the structure design of a tunnel. In this study, the earth pressure and water pressure on the tunnel lining of four cross sections of a metro tunnel were measured and analyzed and then compared with the theoretical values. Results show that the values and distribution of observed ground pressure acting on the lining are different for different overburden depths. The water pressure measured on‐site is approximately equal to the theoretical hydrostatic pressure. The water pressure acting on the shield tunnel lining does not fluctuate with the shield tunnel excavation. The maximum ground pressure was measured in the process of backfill grouting, and the maximum values are approximately larger than 30% of the stable value of the measured pressure. For a shield tunnel under a river with deep water, the water pressure on the lining is dominant and the observed total ground pressure is nearly equal to the water pressure. The findings presented in this paper can provide a reference for the structure design of similar tunnel projects.
Chaotic Color Image Encryption Scheme Using Deoxyribonucleic Acid (DNA) Coding Calculations and Arithmetic over the Galois Field
Authors: Huang Lilian , Wang Shiming , Xiang Jianhong , Sun Yi
Published: March 2020

This paper proposes a chaotic color image encryption scheme based on DNA-coding calculations and arithmetic over the Galois field. Firstly, three modified one-dimensional (1D) chaotic maps with larger key space and better chaotic characteristics are presented. The experimental results show that their chaotic intervals are not only expanded to 0,15, but their average largest Lyapunov Exponent reaches 10. They are utilized as initial keys. Secondly, DNA coding and calculations are applied in order to add more permutation of the cryptosystem. Ultimately, the numeration over the Galois field ensures the effect for the diffusion of pixels. The simulation analysis shows that the encryption scheme proposed in this paper has good encryption effect, and the numerical results verify that it has higher security than some of the latest cryptosystems.
Paracrine Mechanisms of Mesenchymal Stromal Cells in Angiogenesis
Authors: Maacha Selma , Sidahmed Heba , Jacob Shana , Gentilcore Giusy , Calzone Rita , Grivel Jean-Charles , Cugno Chiara
Published: March 2020

The role of the mesenchymal stromal cell- (MSC-) derived secretome is becoming increasingly intriguing from a clinical perspective due to its ability to stimulate endogenous tissue repair processes as well as its effective regulation of the immune system, mimicking the therapeutic effects produced by the MSCs. The secretome is a composite product secreted by MSC in vitro (in conditioned medium) and in vivo (in the extracellular milieu), consisting of a protein soluble fraction (mostly growth factors and cytokines) and a vesicular component, extracellular vesicles (EVs), which transfer proteins, lipids, and genetic material. MSC-derived secretome differs based on the tissue from which the MSCs are isolated and under specific conditions (e.g., preconditioning or priming) suggesting that clinical applications should be tailored by choosing the tissue of origin and a priming regimen to specifically correct a given pathology. MSC-derived secretome mediates beneficial angiogenic effects in a variety of tissue injury-related diseases. This supports the current effort to develop cell-free therapeutic products that bring both clinical benefits (reduced immunogenicity, persistence in vivo, and no genotoxicity associated with long-term cell cultures) and manufacturing advantages (reduced costs, availability of large quantities of off-the-shelf products, and lower regulatory burden). In the present review, we aim to give a comprehensive picture of the numerous components of the secretome produced by MSCs derived from the most common tissue sources for clinical use (e.g., AT, BM, and CB). We focus on the factors involved in the complex regulation of angiogenic processes.
Capturing the Characteristics of Car-Sharing Users: Data-Driven Analysis and Prediction Based on Classification
Authors: Bi Jun , Zhi Ru , Xie Dong-Fan , Zhao Xiao-Mei , Zhang Jun
Published: March 2020

This work explores the characteristics of the usage behaviour of station-based car-sharing users based on the actual operation data from a car-sharing company in Gansu, China. We analyse the characteristics of the users’ demands, such as usage frequency and order quantity, for a day with 24 1 h time intervals. Results show that most car-sharing users are young and middle-aged men with a low reuse rate. The distribution of users’ usage during weekdays shows noticeable morning and evening peaks. We define two attributes, namely, the latent ratio and persistence ratio, as classification indicators to understand the user diversity and heterogeneity thoroughly. We apply the k-means clustering algorithm to group the users into four categories, namely, lost, early loyal, late loyal, and motivated users. The usage characteristics of lost users, including maximum rental time and travel distance, minimum percentage of same pickup and return station, and low percentage of locals, have noticeable differences from those of the other users. Late loyal users have lower rental time and travel distance than those of the other users. This manifestation is in line with the short-term lease of shared cars to complete short- and medium-distance travel design concepts. We also propose a model that predicts the driver cluster based on the decision tree. Numerical tests indicate that the accuracy is 91.61% when the user category is predicted four months in advance using the observation-to-judgment period ratio of 3 : 1. The results in this study can support enterprises in user management.
Soft Clustering for Enhancing the Diagnosis of Chronic Diseases over Machine Learning Algorithms
Authors: Aldhyani Theyazn H.H , Alshebami Ali Saleh , Alzahrani Mohammed Y.
Published: March 2020

Chronic diseases represent a serious threat to public health across the world. It is estimated at about 60% of all deaths worldwide and approximately 43% of the global burden of chronic diseases. Thus, the analysis of the healthcare data has helped health officials, patients, and healthcare communities to perform early detection for those diseases. Extracting the patterns from healthcare data has helped the healthcare communities to obtain complete medical data for the purpose of diagnosis. The objective of the present research work is presented to improve the surveillance detection system for chronic diseases, which is used for the protection of people’s lives. For this purpose, the proposed system has been developed to enhance the detection of chronic disease by using machine learning algorithms. The standard data related to chronic diseases have been collected from various worldwide resources. In healthcare data, special chronic diseases include ambiguous objects of the class. Therefore, the presence of ambiguous objects shows the availability of traits involving two or more classes, which reduces the accuracy of the machine learning algorithms. The novelty of the current research work lies in the assumption that demonstrates the noncrisp Rough K-means (RKM) clustering for figuring out the ambiguity in chronic disease dataset to improve the performance of the system. The RKM algorithm has clustered data into two sets, namely, the upper approximation and lower approximation. The objects belonging to the upper approximation are favourable objects, whereas the ones belonging to the lower approximation are excluded and identified as ambiguous. These ambiguous objects have been excluded to improve the machine learning algorithms. The machine learning algorithms, namely, naïve Bayes (NB), support vector machine (SVM), K-nearest neighbors (KNN), and random forest tree, are presented and compared. The chronic disease data are obtained from the machine learning repository and Kaggle to test and evaluate the proposed model. The experimental results demonstrate that the proposed system is successfully employed for the diagnosis of chronic diseases. The proposed model achieved the best results with naive Bayes with RKM for the classification of diabetic disease (80.55%), whereas SVM with RKM for the classification of kidney disease achieved 100% and SVM with RKM for the classification of cancer disease achieved 97.53 with respect to accuracy metric. The performance measures, such as accuracy, sensitivity, specificity, precision, and F-score, are employed to evaluate the performance of the proposed system. Furthermore, evaluation and comparison of the proposed system with the existing machine learning algorithms are presented. Finally, the proposed system has enhanced the performance of machine learning algorithms.
Weakly Supervised GAN for Image-to-Image Translation in the Wild
Authors: Cao Zhiyi , Niu Shaozhang , Zhang Jiwei
Published: March 2020

Generative Adversarial Networks (GANs) have achieved significant success in unsupervised image-to-image translation between given categories (e.g., zebras to horses). Previous GANs models assume that the shared latent space between different categories will be captured from the given categories. Unfortunately, besides the well-designed datasets from given categories, many examples come from different wild categories (e.g., cats to dogs) holding special shapes and sizes (short for adversarial examples), so the shared latent space is troublesome to capture, and it will cause the collapse of these models. For this problem, we assume the shared latent space can be classified as global and local and design a weakly supervised Similar GANs (Sim-GAN) to capture the local shared latent space rather than the global shared latent space. For the well-designed datasets, the local shared latent space is close to the global shared latent space. For the wild datasets, we will get the local shared latent space to stop the model from collapse. Experiments on four public datasets show that our model significantly outperforms state-of-the-art baseline methods.
Extension of Optimal Homotopy Asymptotic Method with Use of Daftardar–Jeffery Polynomials to Coupled Nonlinear-Korteweg-De-Vries System
Authors: Nawaz Rashid , Hussain Zawar , Khattak Abraiz , Khan Adam
Published: March 2020

In this paper, Daftardar–Jeffery Polynomials are introduced in the Optimal Homotopy Asymptotic Method for solution of a coupled system of nonlinear partial differential equations. The coupled nonlinear KdV system is taken as test example. The results obtained by the proposed method are compared with the multistage Optimal Homotopy Asymptotic Method. The results show the efficiency and consistency of the proposed method over the Optimal Homotopy Asymptotic Method. In addition, accuracy of the proposed method can be improved by taking higher order approximations.