Elliptic flow of charged particles in Pb-Pb collisions at sqrt[S(NN)] = 2.76 TeV

We report the first measurement of charged particle elliptic flow in Pb-Pb collisions at sqrt[S(NN)] =2.76 TeV with the ALICE detector at the CERN Large Hadron Collider. The measurement is performed in the central pseudorapidity region (|η|<0.8) and transverse momentum range 0.2<p t<5.0 GeV/c. The elliptic flow signal v₂, measured using the 4-particle correlation method, averaged over transverse momentum and pseudorapidity is 0.087 ± 0.002(stat) ± 0.003(syst) in the 40%-50% centrality class. The differential elliptic flow v₂ p t reaches a maximum of 0.2 near p t =3 GeV/c. Compared to RHIC Au-Au collisions at sqrt[S(NN)] 200 GeV, the elliptic flow increases by about 30%. Some hydrodynamic model predictions which include viscous corrections are in agreement with the observed increase.

Centrality dependence of the charged-particle multiplicity density at midrapidity in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

The centrality dependence of the charged-particle multiplicity density at midrapidity in Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV is presented. The charged-particle density normalized per participating nucleon pair increases by about a factor of 2 from peripheral (70%-80%) to central (0%-5%) collisions. The centrality dependence is found to be similar to that observed at lower collision energies. The data are compared with models based on different mechanisms for particle production in nuclear collisions.

Higher harmonic anisotropic flow measurements of charged particles in Pb-Pb collisions at sqrt(s(NN)) = 2.76 TeV

We report on the first measurement of the triangular v3, quadrangular v4, and pentagonal v5 charged particle flow in Pb-Pb collisions at sqrt(s(NN)) = 2.76  TeV measured with the ALICE detector at the CERN Large Hadron Collider. We show that the triangular flow can be described in terms of the initial spatial anisotropy and its fluctuations, which provides strong constraints on its origin. In the most central events, where the elliptic flow v2 and v3 have similar magnitude, a double peaked structure in the two-particle azimuthal correlations is observed, which is often interpreted as a Mach cone response to fast partons. We show that this structure can be naturally explained from the measured anisotropic flow Fourier coefficients.

Charged-particle multiplicity density at midrapidity in central Pb-Pb collisions at sqrt[S(NN)] = 2.76 TeV

The first measurement of the charged-particle multiplicity density at midrapidity in Pb-Pb collisions at a center-of-mass energy per nucleon pair √ S NN = 2.76 TeV is presented. For an event sample corresponding to the most central 5% of the hadronic cross section, the pseudorapidity density of primary charged particles at midrapidity is 1584 ± 4(stat) ± 76(syst), which corresponds to 8.3 ± 0.4(syst) per participating nucleon pair. This represents an increase of about a factor 1.9 relative to pp collisions at similar collision energies, and about a factor 2.2 to central Au-Au collisions at √ S NN = 2.76 TeV. This measurement provides the first experimental constraint for models of nucleus-nucleus collisions at LHC energies.

Laparoscopic visualization of the cystic artery anatomy

Uncontrolled bleeding from the cystic artery and its branches is a serious problem that may increase the risk of intraoperative lesions to vital vascular and biliary structures. On laparoscopic visualization anatomic relations are seen differently than during conventional surgery, so proper knowledge of the hepatobiliary triangle anatomic structures under the conditions of laparoscopic visualization is required. We present an original classification of the anatomic variations of the cystic artery into two main groups based on our experience with 200 laparoscopic cholecystectomies, with due consideration of the known anatomicotopographic relations. Group I designates a cystic artery situated within the hepatobiliary triangle on laparoscopic visualization. This group included three types: (1) normally lying cystic artery, found in 147 (73.5%) patients; (2) most common cystic artery variation, manifesting as its doubling, present in 31 (15.5%) patients; and (3) the cystic artery originating from the aberrant right hepatic artery, observed in 11 (5.5%) patients. Group II designates a cystic artery that could not be found within the hepatobiliary triangle on laparoscopic dissection. This group included two types of variation: (1) cystic artery originating from the gastroduodenal artery, found in nine (4. 5%) patients; and (2) cystic artery originating from the left hepatic artery, recorded in two (1%) patients.

Charmonium and e+e- pair photoproduction at mid-rapidity in ultra-peripheral Pb-Pb collisions at [Formula: see text]

The ALICE Collaboration at the LHC has measured the J/ψ and ψ' photoproduction at mid-rapidity in ultra-peripheral Pb-Pb collisions at [Formula: see text]. The charmonium is identified via its leptonic decay for events where the hadronic activity is required to be minimal. The analysis is based on an event sample corresponding to an integrated luminosity of about 23 μb-1. The cross section for coherent and incoherent J/ψ production in the rapidity interval -0.9 Collapse

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Emerging Therapeutic Potential of Mesenchymal Stem/Stromal Cells in Preeclampsia

PURPOSE OF REVIEW

Preeclampsia is a dangerous pregnancy condition affecting both the mother and offspring. It is a multifactorial disease with poorly understood pathogenesis, lacking effective treatments. Maternal immune response, inflammation and oxidative stress leading to endothelial dysfunction are the most prominent pathogenic processes implicated in preeclampsia development. Here, we give a detailed overview of the therapeutic applications and mechanisms of mesenchymal stem/stromal cells (MSCs) as a potential new treatment for preeclampsia.

RECENT FINDINGS

MSCs have gained growing attention due to low immunogenicity, easy cultivation and expansion in vitro. Accumulating evidence now suggests that MSCs act primarily through their secretomes facilitating paracrine signalling that leads to potent immunomodulatory, pro-angiogenic and regenerative therapeutic effects. MSCs have been studied in different animal models of preeclampsia demonstrating promising result, which support further investigations into the therapeutic effects and mechanisms of MSC-based therapies in preeclampsia, steering these therapies into clinical trials.

LongStitch: high-quality genome assembly correction and scaffolding using long reads

BACKGROUND

Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads.

RESULTS

LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM.

CONCLUSIONS

Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch .

J/ψ suppression at forward rapidity in Pb-Pb collisions at √s(NN) = 2.76 TeV

The ALICE experiment has measured the inclusive J/ψ production in Pb-Pb collisions at √s(NN) = 2.76 TeV down to zero transverse momentum in the rapidity range 2.5 < y < 4. A suppression of the inclusive J/ψ yield in Pb-Pb is observed with respect to the one measured in pp collisions scaled by the number of binary nucleon-nucleon collisions. The nuclear modification factor, integrated over the 0%-80% most central collisions, is 0.545 ± 0.032(stat) ± 0.083(syst) and does not exhibit a significant dependence on the collision centrality. These features appear significantly different from measurements at lower collision energies. Models including J/ψ production from charm quarks in a deconfined partonic phase can describe our data.

Volume changes of corpus striatum, thalamus, hippocampus and lateral ventricles in posttraumatic stress disorder (PTSD) patients suffering from headaches and without therapy

BACKGROUND AND AIM

In the present study, we have hypothesized that volume changes of the caudate nucleus, putamen, globus pallidus, hippocampus, thalamus, and lateral ventricle in newly-diagnosed, male PTSD patients without therapy are more pronounced in those with headaches. To confirm or reject our hypothesis, we have undertaken an extensive study of forty-nine PTSD patients.

PATIENTS AND METHODS

To confirm or reject our hypothesis, we have undertaken an extensive study of forty-nine PTSD male patients that underwent MRI scanning immediately upon admittance for the treatment. Based on headache frequency, they were classified into three groups: group 1 included patients with headaches at least twice a week; group 2 consisted of patients with headaches less than twice a week; and group 3 consisted of patients without headaches. All MRI scans underwent software-based volume compute and statistical processing.

RESULTS

39 out of 49 patients with PTSD suffered from headaches. Bilaterally, volume decreases were noted in groups 1 and 2 compared to group 3 for the caudate nucleus, putamen, hippocampus and lateral ventricle. Differences in globus pallidus and thalamus among groups appeared to be insignificant.

CONCLUSION

The present study revealed a bilateral volume decrease of the caudate nucleus, putamen and hippocampus in PTSD male subjects without therapy. Intensity of volume alterations correlated with Hamilton's depression rating score; regression analysis uncovered correlated changes in the caudate nucleus, putamen and hippocampus, and an inverse correlation with the volume of the lateral ventricle in the PTSD patients.

Charge separation relative to the reaction plane in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

Measurements of charge-dependent azimuthal correlations with the ALICE detector at the LHC are reported for Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV. Two- and three-particle charge-dependent azimuthal correlations in the pseudorapidity range |η| < 0.8 are presented as a function of the collision centrality, particle separation in pseudorapidity, and transverse momentum. A clear signal compatible with a charge-dependent separation relative to the reaction plane is observed, which shows little or no collision energy dependence when compared to measurements at RHIC energies. This provides a new insight for understanding the nature of the charge-dependent azimuthal correlations observed at RHIC and LHC energies.

Biodegradation of polystyrene-graft-starch copolymers in three different types of soil

Materials based on polystyrene and starch copolymers are used in food packaging, water pollution treatment, and textile industry, and their biodegradability is a desired characteristic. In order to examine the degradation patterns of modified, biodegradable derivates of polystyrene, which may keep its excellent technical features but be more environmentally friendly at the same time, polystyrene-graft-starch biomaterials obtained by emulsion polymerization in the presence of new type of initiator/activator pair (potassium persulfate/different amines) were subjected to 6-month biodegradation by burial method in three different types of commercially available soils: soil rich in humus and soil for cactus and orchid growing. Biodegradation was monitored by mass decrease, and the highest degradation rate was achieved in soil for cactus growing (81.30%). Statistical analysis proved that microorganisms in different soil samples have different ability of biodegradation, and there is a significant negative correlation between the share of polystyrene in copolymer and degree of biodegradation. Grafting of polystyrene on starch on one hand prevents complete degradation of starch that is present (with maximal percentage of degraded starch ranging from 55 to 93%), while on the other hand there is an upper limit of share of polystyrene in the copolymer (ranging from 37 to 77%) that is preventing biodegradation of degradable part of copolymers.

Pion, kaon, and proton production in central Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

In this Letter we report the first results on π(±), K(±), p, and p production at midrapidity (|y|<0.5) in central Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV, measured by the ALICE experiment at the LHC. The p(T) distributions and yields are compared to previous results at sqrt[s(NN)] = 200 GeV and expectations from hydrodynamic and thermal models. The spectral shapes indicate a strong increase of the radial flow velocity with sqrt[s(NN)], which in hydrodynamic models is expected as a consequence of the increasing particle density. While the K/π ratio is in line with predictions from the thermal model, the p/π ratio is found to be lower by a factor of about 1.5. This deviation from thermal model expectations is still to be understood.

D meson elliptic flow in noncentral Pb-Pb collisions at sqrt[sNN]=2.76 Tev

Azimuthally anisotropic distributions of D0, D+, and D*+ mesons were studied in the central rapidity region (|y|<0.8) in Pb-Pb collisions at a center-of-mass energy sqrt[sNN]=2.76  TeV per nucleon-nucleon collision, with the ALICE detector at the LHC. The second Fourier coefficient v2 (commonly denoted elliptic flow) was measured in the centrality class 30%-50% as a function of the D meson transverse momentum pT, in the range 2-16  GeV/c. The measured v2 of D mesons is comparable in magnitude to that of light-flavor hadrons. It is positive in the range 2<pT<6  GeV/c with 5.7σ significance, based on the combination of statistical and systematic uncertainties.

Measurement of inelastic, single- and double-diffraction cross sections in proton-proton collisions at the LHC with ALICE

Measurements of cross sections of inelastic and diffractive processes in proton-proton collisions at LHC energies were carried out with the ALICE detector. The fractions of diffractive processes in inelastic collisions were determined from a study of gaps in charged particle pseudorapidity distributions: for single diffraction (diffractive mass MX <200 GeV/c2) [Formula: see text], and [Formula: see text], respectively at centre-of-mass energies [Formula: see text]; for double diffraction (for a pseudorapidity gap Δη>3) σDD/σINEL=0.11±0.03,0.12±0.05, and [Formula: see text], respectively at [Formula: see text]. To measure the inelastic cross section, beam properties were determined with van der Meer scans, and, using a simulation of diffraction adjusted to data, the following values were obtained: [Formula: see text] mb at [Formula: see text] and [Formula: see text] at [Formula: see text]. The single- and double-diffractive cross sections were calculated combining relative rates of diffraction with inelastic cross sections. The results are compared to previous measurements at proton-antiproton and proton-proton colliders at lower energies, to measurements by other experiments at the LHC, and to theoretical models.

Transverse momentum distribution and nuclear modification factor of charged particles in p+Pb collisions at sqrt[s(NN)] = 5.02 TeV

The transverse momentum (p(T)) distribution of primary charged particles is measured in minimum bias (non-single-diffractive) p+Pb collisions at sqrt[s(NN)]=5.02 TeV with the ALICE detector at the LHC. The p(T) spectra measured near central rapidity in the range 0.5<p(T) <20 GeV/c exhibit a weak pseudorapidity dependence. The nuclear modification factor R(pPb) is consistent with unity for p(T) above 2 GeV/c. This measurement indicates that the strong suppression of hadron production at high p(T) observed in Pb+Pb collisions at the LHC is not due to an initial-state effect. The measurement is compared to theoretical calculations.

Epidemiology and risk factors for multi-drug resistant hospital-acquired urinary tract infection in patients with liver cirrhosis: single center experience in Serbia

Background

Cirrhosis-associated immune dysfunction syndrome (CAIDS) has been identified in patients with liver cirrhosis (LC), predisposing them to a wide variety of infections. In patients with LC, healthcare-associated infections involving multi-drug resistant (MDR) bacteria have increased significantly over the last decades. Among them, hospital-acquired urinary tract infections (HA-UTI) are the most common. This study aimed to investigate the rates of antimicrobial resistance among patients with LC and HA-UTI and to determine risk factors associated with their development among patients hospitalized in tertiary care facility in Serbia.

Methods

This retrospective study included 65 hospitalized patients with LC who had developed HA-UTI. We examined the epidemiology of these infections concerning resistance to the most commonly used antimicrobials and patient-specific risk factors associated with HA-UTI development by MDR pathogens.

Results

The most frequently isolated organisms were Enterococcus spp. (n = 34, 52.3%), Klebsiella spp. (n = 10, 15.4%), and E.coli (n = 6, 9.2%). Thirty-five isolates (53.8%) were identified as MDR, and 30 (46.2%) were non-MDR.We found a statistically significant difference in the distribution of MDR and non-MDR strains, based on Gram staining, with the majority of Gram-negative pathogens being MDR (p = 0.005). We identified age ≥ 65 years (p = 0.007), previous use of cephalosporins as empiric therapy (p = 0.042), and the presence of hepatic encephalopathy (p = 0.011) as independent risk factors for the development of MDR UTIs.

Conclusion

This is the first study from Serbia and the Balkans concerning the changing epidemiology of MDR UTI in patients with LC. Our study showed that more than half of HA-UTI was caused by MDR and the most common pathogen was Enterococcus spp. The overall resistance to ceftriaxone was 92%. Our findings underscore the need for institutions to individualize protocols for treatment of hospital-acquired infections, particularly in immunocompromised populations.

Pseudorapidity density of charged particles in p+Pb collisions at √(s(NN))=5.02 TeV

The charged-particle pseudorapidity density measured over four units of pseudorapidity in nonsingle-diffractive p+Pb collisions at a center-of-mass energy per nucleon pair √(s(NN))=5.02 TeV is presented. The average value at midrapidity is measured to be 16.81±0.71 (syst), which corresponds to 2.14±0.17 (syst) per participating nucleon, calculated with the Glauber model. This is 16% lower than in nonsingle-diffractive pp collisions interpolated to the same collision energy and 84% higher than in d+Au collisions at s√(s(NN))=0.2 TeV. The measured pseudorapidity density in p+Pb collisions is compared to model predictions and provides new constraints on the description of particle production in high-energy nuclear collisions.

Topoanatomic relations of the ophthalmic artery viewed in four horizontal layers

In the present paper we have studied the gross anatomy of the ophthalmic artery in 200 human cadaver dissections viewed in four horizontal layers. The ophthalmic artery can be divided into the origin, intracranial, intracanalicular and intraorbital parts. The most common origin of the artery was from the medial half of the anterior side of the internal carotid artery (ICA) in its upper curve (52%), followed by the medial half of the superior side (44%), and in only 4% from the medial side of the upper curve of the ICA. We have examined the topographic anatomy of the ophthalmic artery in detail, and found a rare anastomosis of the ophthalmic artery with the frontal branch of the middle meningeal artery.

Prognostic Factors for Post-Recurrence Survival in Stage II and III Colorectal Carcinoma Patients

Background and objectives: This study aimed to evaluate prognostic factors for post-recurrence survival in local and locally advanced colorectal cancer patients. Materials and Methods: A total of 273 patients with stage III and high-risk stage II colorectal cancer were prospectively enrolled. All patients underwent operative treatment of the primary tumor and adjuvant fluorouracil-based chemotherapy. Results: Over the three-year period (2008–2010), a cohort of 273 patients with stage III and high-risk stage II colorectal cancer had been screened. During follow up, 105 (38.5%) patients had disease recurrence. Survival rates 1-, 3- and 5-year after recurrence were 53.9, 18.2 and 6.5%, respectively, and the median post-recurrence survival time was 13 months. Survival analysis showed that age at diagnosis (p < 0.01), gender (p < 0.05), elevated postoperative Ca19-9 (p < 0.01), tumor histology (adenocarcinoma vs. mucinous vs. signet ring tumors, p < 0.01) and tumor stage (II vs. III, p < 0.05) had a significant influence on post-recurrence survival. Recurrence interval and metastatic site were not related to survival following recurrence. Multivariate analysis showed that older age (HR 2.43), mucinous tumors (HR 1.51) and tumors expressing Ca19-9 at baseline (HR 3.51) were independently associated with survival following recurrence. Conclusions: Baseline patient and tumor characteristics largely predicted patient outcomes after disease recurrence. Recurrence intervals in local and locally advanced colorectal cancer were not found to be prognostic factors for post-recurrence survival. Older age, male gender, stage III and mucinous histology were poor prognostic factors after the disease had recurred. Stage II patients had remarkable post-recurrence survival compared to stage III patients.

Functional characterization of the muscarinic receptors involved in endothelium-dependent relaxation in isolated canine uterine artery

Acetylcholine interacts with endothelial muscarinic receptors releasing nitric oxide and causing vasodilatation. To identify the receptor subtype responsible for acetylcholine-induced relaxation in canine uterine artery, the usual organ bath method for in vitro investigation on isolated blood vessels was applied. Using a range of muscarinic receptor antagonists such as atropine (nonselective), pirenzepine (M(1)-selective), methoctramine (M(2)-selective) and p-fluoro-hexahydro-sila-difenidol (p-FHHSiD) (M(1)/M(3)) and determining pA2 value of those antagonists through Shild analysis, we aimed at establishing a precise receptor mechanism underlying acetylcholine-induced relaxation in isolated canine uterine artery. The relaxation of uterine arterial rings in response to acetylcholine in the presence or absence of selective muscarinic receptors antagonists was calculated using concentration response curves. Acetylcholine induced concentration-dependent and endothelium-dependent relaxation of arterial rings precontracted with phenylephrine (pEC(50) = 6.90 +/- 0.02). Muscarinic receptors antagonists atropine, pirenzepine, methoctramine and p-FHHSiD competitively antagonized the response to acetylcholine and obtained pA(2) values were 9.91 +/- 0.06, 6.60 +/- 0.04, 6.21 +/- 0.08 and 8.05 +/- 0.1, respectively. This study showed that acetylcholine induced endothelium-dependent relaxation of canine uterine artery by stimulation of muscarinic receptors localized on the endothelial cells. On the basis of differential antagonist affinity, we suggest that the muscarinic receptors involved in the acetylcholine-induced relaxation of canine uterine artery are predominantly of M(3) subtype.

Measurement of the cross section for electromagnetic dissociation with neutron emission in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

The first measurement of neutron emission in electromagnetic dissociation of ^{208}Pb nuclei at the LHC is presented. The measurement is performed using the neutron zero degree calorimeters of the ALICE experiment, which detect neutral particles close to beam rapidity. The measured cross sections of single and mutual electromagnetic dissociation of Pb nuclei at sqrt[s(NN)]=2.76 TeV with neutron emission are σ(singleEMD)=187.4 ± 0.2(stat)(-11.2)(+13.2) (syst) b and σ(mutualEMD) = 5.7 ± 0.1(stat) ± 0.4(syst) b, respectively. The experimental results are compared to the predictions from a relativistic electromagnetic dissociation model.

Quality of life following two different techniques of an open ventral hernia repair for large hernias: a prospective randomized study

Background

We compare the health-related quality of life (QoL) of patients with incision hernias before and after surgery with two different techniques.

Methods

In this prospective randomized study, the study population consisted of all patients who underwent the first surgical incisional hernias repair during the 1-year study period. Patients who met the criteria for inclusion in the study were randomized into two groups: the first group consisted of patients operated by an open Rives sublay technique, and the second group included patients operated by a segregation component technique. The change in the quality of life before and 6 months after surgery was assessed using two general (Short form of SF-36 questionnaires and European Quality of Life Questionnaire—EQ-5D-3L), and three specific hernia questionnaires (Hernia Related Quality of Life Survey-HerQles, Eura HS Quality of Life Scale—EuraHS QoL, and Carolinas Comfort Scale—CCS).

Results

A total of 93 patients were included in the study. Patients operated on by the Rives technique had a better role physical score before surgery, according to the SF-36 tool, although this was not found after surgery. The postoperative QoL measured with each scale of all questionnaires was significantly better after surgery. Comparing two groups of patients after surgery, only the pain domain of the EuraHS Qol questionnaire was worse in patients operated by a segregation component technique.

Conclusion

Both techniques improve the quality of life after surgery. Generic QoL questionnaires showed no difference in the quality of life compared to repair technique but specific hernia-related questionnaires showed differences.

ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling, and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: ntLink scaffolding using overlap detection Basic Protocol 2: ntLink scaffolding with gap-filling Basic Protocol 3: Running in-code iterations of ntLink scaffolding Alternate Protocol 1: Generating long-read to contig mappings with ntLink Alternate Protocol 2: Using ntLink mappings for genome assembly correction with Tigmint-long Support Protocol: Installing ntLink.

J/ψ elliptic flow in Pb-Pb collisions at √(s(NN))=2.76 TeV

We report on the first measurement of inclusive J/ψ elliptic flow v2 in heavy-ion collisions at the LHC. The measurement is performed with the ALICE detector in Pb-Pb collisions at √(s(NN))=2.76 TeV in the rapidity range 2.5<y<4.0. The dependence of the J/ψ v2 on the collision centrality and on the J/ψ transverse momentum is studied in the range 0≤p(T)<10 GeV/c. For semicentral Pb-Pb collisions at √(s(NN))=2.76 TeV, an indication of nonzero v2 is observed with a largest measured value of v2=0.116±0.046(stat)±0.029(syst) for J/ψ in the transverse momentum range 2≤p(T)<4 GeV/c. The elliptic flow measurement complements the previously reported ALICE results on the inclusive J/ψ nuclear modification factor and favors the scenario of a significant fraction of J/ψ production from charm quarks in a deconfined partonic phase.