bluuebunny/crossref_metadata_2025_split huggingface dataset:
Superfluidity and coherence in uniform dipolar binary Bose mixtures
Authors: Boudjemâa Abdelâali 
Published: September 2020

Abstract
We investigate the superfluidity and the coherence in dipolar binary Bose mixtures using the hydrodynamic approach. Useful analytical formulas for the excitation spectra, the first-order correlation function, the static structure factor, and the superfluid fraction are derived. We find that in the case of highly imbalanced mixture, the superfluidity can occur in the dilute component only at extremely low temperatures. The behavior of the first-order correlation function for both dipolar and nondipolar Bose mixtures is deeply analyzed. Then we face the two-dimensional case which encodes a non-trivial physics due to the roton modes.
Diffusive search for a stochastically-gated target with resetting
Authors: Bressloff Paul C 
Published: September 2020

Abstract
In this paper, we analyze the mean first passage time (MFPT) for a single Brownian particle to find a stochastically-gated target under the additional condition that the position of the particle is reset to its initial position
x

0 at a rate r. The gate switches between an open (absorbing) and closed (reflecting) state according to a two-state Markov chain and can only be detected by the searcher in the open state. One possible example of such a target is a protein switching between different conformational states. As expected, the MFPT with or without resetting is an increasing function of the fraction of time ρ
0 that the gate is closed or reflecting. However, the interplay between stochastic resetting and stochastic gating has non-trivial effects with regards the optimization of the search process under resetting. First, by considering the diffusive search for a gated target at one end of an interval, we show that the ratio Δ(r) = T(r)/T(0), where T(r) is the MFPT at a resetting rate r, exhibits a non-monotonic dependence on ρ
0 even though T(r) and T(0) increase monotonically with ρ
0. In particular, the value of Δ(r) at the optimal resetting rate (when it exists) decreases with ρ
0 up to some critical value, after which it increases and eventually approaches unity. Second, in the case of a spherical target in

R

d

, the dependence of the MFPT on the spatial dimension d is significantly amplified in the presence of stochastic gating.
The statistical foundation of entropy in extended irreversible thermodynamics
Authors: Hong Liu , Qian Hong 
Published: September 2020

Abstract
In the theory of extended irreversible thermodynamics (EIT), the flux-dependent entropy function plays a key role; it is a fundamental distinction between EIT and the usual flux-independent entropy function adopted by classical irreversible thermodynamics (CIT). However, its existence, as a prerequisite for EIT, and its statistical origin have never been justified. In this work, by studying the macroscopic limit of an ϵ-dependent Langevin dynamics, which admits a large deviations (LD) principle, we show that the stationary LD rate functions of probability density p

ϵ
(x, t) and joint probability density

p

ϵ

(

x
,

x

̇

,
t

)

actually turn out to be the desired flux-independent entropy function in CIT and flux-dependent entropy function in EIT respectively. The difference of the two entropy functions is determined by the time resolution for Brownian motions times a Lagrangian, the latter arises from the LD Hamilton–Jacobi equation and can be used for constructing conserved Lagrangian/Hamiltonian dynamics.
Brightening of spin- and momentum-dark excitons in transition metal dichalcogenides
Authors: Feierabend Maja , Brem Samuel , Ekman August , Malic Ermin 
Published: September 2020

Abstract
Monolayer transition metal dichalcogenides (TMDs) have been in focus of current research, among others due to their remarkable exciton landscape consisting of bright and dark excitonic states. Although dark excitons are not directly visible in optical spectra, they have a large impact on exciton dynamics and hence their understanding is crucial for potential TMD-based applications. Here, we study brightening mechanisms of dark excitons via interaction with phonons and in-plane magnetic fields. We show clear signatures of momentum- and spin-dark excitons in WS2, WSe2 and MoS2, while the photoluminescence of MoSe2 is only determined by the bright exciton. In particular, we reveal the mechanism behind the brightening of states that are both spin- and momentum-dark in MoS2. Our results are in good agreement with recent experiments and contribute to a better microscopic understanding of the exciton landscape in TMDs.
Manipulation of DNA transport through solid-state nanopores by atomic force microscopy
Authors: Si Wei , Yang Haojie , Wu Gensheng , Chen Chang , Yu Meng 
Published: September 2020

Abstract
To realize DNA sequencing by a solid-state nanopore, the translocation speed of DNA through the nanopore should be slowed down to obtain the temporal resolution. In this study, we make a nanopore sensing system integrated with an atomic force microscope to control DNA transport through solid-state nanopores. The speed of DNA bound to the probe tip through the nanopore can be controlled by manipulating AFM probe tip, the ionic current as well as the force exerted on DNA strand while it is translocating through the nanopore could be simultaneously measured by the integrated system. The velocity of DNA molecules could be slowed down to ∼100 nm s−1, much less than 1 nt ms−1, which fully meets the requirement for nanopore DNA sequencing. When the probe tip is moving toward or away from the nanopore, obvious current steps associated with force steps are observed during the capturing and releasing processes of DNA strands. All-atom molecular dynamics simulation further validates the observed correlation between the ionic current and dragging force when the DNA is moving through the nanopore.
Influence of heat treatments on microstructure, mechanical properties and corrosion resistance of Inconel 625 overlay cladded using PTIG
Authors: Guo Longlong , Xiao Fei , Wang Fan , Wei Wenlan , He Yutian , Luo Foshu 
Published: September 2020

Abstract
The influence of post-weld heat treatment (PWHT) temperatures on the microstructure, mechanical properties and corrosion resistance of Inconel 625 overlay cladded using pulsed tungsten insert gas (PTIG) was studied. The microstructure observation shows that as welded Inconel 625 overlay exhibits notable difference in grains morphology and size, and some precipitates, such as laves phase and MC phase, are distributed in the interdendritic zone. With an increase in PWHT temperature, equiaxed dendrites transform to columnar dendrites, and the overall difference in the microstructure decreases gradually. Compared with the as welded overlay, the size and number of the precipitates for the overlay heat treated at 650 °C shows very slight change. When the PWHT temperature increases to 750 °C, δ phase precipitates with the dissolving of laves phase. The number of δ phase increases clearly, and its size coarsens obviously with a further increasing PWHT temperature. Tensile tests indicate that there is a slight increase in the yield strength (YS) and ultimate tensile strength (UTS), but a decrease in elongation with the raise of PWHT temperature, which is no greater than 750 °C. Conversely, when the PWHT temperature beyond 750 °C, the YS and UTS decrease, the elongation increases slightly. Corrosion tests in the environment containing H2S and CO2 reveal that the Inconel 625 overlay heat treated at 650 °C exhibits superior corrosion resistance than that of other temperatures. Whereas, with an increase in PWHT temperature, the corrosion resistance degenerates seriously for the formation of δ phase.
NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling
Authors: Menzel Michael , Hurka Sabine , Glasenhardt Stefan , Gogol-Döring Andreas 
Published: September 2020

Abstract

Motivation
The discovery of sequence motifs mediating DNA-protein binding usually implies the determination of binding sites using high-throughput sequencing and peak calling. The determination of peaks, however, depends strongly on data quality and is susceptible to noise.

Results
Here, we present a novel approach to reliably identify transcription factor-binding motifs from ChIP-Seq data without peak detection. By evaluating the distributions of sequencing reads around the different k-mers in the genome, we are able to identify binding motifs in ChIP-Seq data that yield no results in traditional pipelines.

Availability and implementation
NoPeak is published under the GNU General Public License and available as a standalone console-based Java application at https://github.com/menzel/nopeak.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cyber conflict or democracy “hacked”? How cyber operations enhance information warfare
Authors: Whyte Christopher 
Published: September 2020

Abstract
Are cyber-enabled information warfare (IW) campaigns uniquely threatening when compared with traditional influence operations undertaken by state actors? Or is the recent “hacking” of Western democracies simply old wine in new—but fundamentally similar—bottles? This article draws on classical theories of democratic functionality from the political science and communications studies fields to deconstruct the aims and effects of cyber-enabled IW. I describe democracies as information systems wherein the moderating functions of democratic discourse and policy deliberation rely on robust mechanisms for asserting the credibility, origination, and quality of information. Whereas the institutions of democracy are often compromised in ways that force failures of the system’s moderating dynamics, influence operations in the digital age act to subvert the traditional mechanisms of democratic functionality in new ways. Sophisticated digital age information operations create a multifaceted attribution challenge to the target state that amounts to unprecedented uncertainty about the nature and scope of the threat. However, the promise of cyber-enabled IW capabilities emerges more from the rewiring of modern democratic information environments around new media platforms than it does from the cyber conflict faculties of state actors. Rather, cyber operations act as an adjunct modifier of IW abilities that allow belligerent governments to secure new sources of private information, to divert attention from other pillars of IW campaigns, to compromise the capabilities of domestic counterintelligence assets and to tacitly coerce important members of society.
Improving vulnerability remediation through better exploit prediction
Authors: Jacobs Jay , Romanosky Sasha , Adjerid Idris , Baker Wade 
Published: September 2020

Abstract
Despite significant innovations in IT security products and research over the past 20 years, the information security field is still immature and struggling. Practitioners lack the ability to properly assess cyber risk, and decision-makers continue to be paralyzed by vulnerability scanners that overload their staff with mountains of scan results. In order to cope, firms prioritize vulnerability remediation using crude heuristics and limited data, though they are still too often breached by known vulnerabilities for which patches have existed for months or years. And so, the key challenge firms face is trying to identify a remediation strategy that best balances two competing forces. On one hand, it could attempt to patch all vulnerabilities on its network. While this would provide the greatest ‘coverage’ of vulnerabilities patched, it would inefficiently consume resources by fixing low-risk vulnerabilities. On the other hand, patching a few high-risk vulnerabilities would be highly ‘efficient’, but may leave the firm exposed to many other high-risk vulnerabilities. Using a large collection of multiple datasets together with machine learning techniques, we construct a series of vulnerability remediation strategies and compare how each perform in regard to trading off coverage and efficiency. We expand and improve upon the small body of literature that uses predictions of ‘published exploits’, by instead using ‘exploits in the wild’ as our outcome variable. We implement the machine learning models by classifying vulnerabilities according to high- and low-risk, where we consider high-risk vulnerabilities to be those that have been exploited in actual firm networks.
461 AMOUNTS OF FAT AND PROTEIN CONSUMPTION ARE HIGHER, BUT OF POLYUNSATURATED FATS LOWER IN CHILDREN WITH GERD COMPARED TO CONTROLS
Authors: Morozov S , Borodina G , Nikityuk D 
Published: September 2020

Abstract

In contrast to adults, characteristic features of diet in children with GERD are not widely studied. Still, they may play an important role in pathogenesis of the disease and are important from the viewpoint of possible non-pharmacological treatment.
The aim of the study was to compare the rates of nutrients consumption in children and adolescents with gastroesophageal reflux disease (GERD) compared to the control group without the disease.

Methods
Based on symptom evaluation and esophageal pH-impedance recordings patients were allocated on to GERD and control groups. All patients underwent esophagogastroscopy. Levels of nutrients consumption were assessed with the use of food frequency questionnaire in the regard to the presence of the disease, oesophagitis, and z-score body mass index (BMI).

Results
Data of 219 children and adolescents were available for the final analysis. Energy values of the rations and amount of fat consumption were higher in the GERD group compared to the control when rations were compared according to z-score BMI. In contrast to nonerosive form of GERD, patients with erosive esophagitis consumed more protein (percentage deviation from the recommended daily allowance Me [25%;75%]): 14.3 (11.07; 19.1) % vs 8.5 (6.71; 14.1) %, total fat 36.8 (12.5; 75.5) % versus 16.9 (10.1; 17.9) %, and less polyunsaturated fats −54.3 (−73.4; −47.7) % vs −45.6 (−56.2; −33.1) %, P &lt; 0.05.

Conclusion
The rations of children with GERD are characterized by higher calorie values and larger amounts of fat intake compared to the control group in the regard to z score BMI. Low dietary fibre consumption is additional factor associated with GERD in children with excessive weight and obesity. Compared to nonerosive GERD, higher intake of energy, protein, and total fat and lower of polyunsaturated fats revealed in patients with GERD with erosive esophagitis.
506 TO STUDY THE CLINICAL IMPACT AND PROGNOSTIC VALUE OF TUMOR INFILTRATING LYMPHOCYTES IN ESOPHAGEAL SQUAMOUS CELL CARCINOMA
Authors: Uma Baskaran N , M A , Rajendiran S 
Published: September 2020

Abstract

Esophageal cancer is the sixth most common cause of death due to cancer worldwide, of which Esophageal Squamous cell carcinoma (ESCC) is the most prevalent type.
The presence of Tumour Infiltrating Lymphocytes (TILs) in a tumour indicates a good prognosis of the cancer following immunotherapy.
Numeral immunological inhibitors have been developed to treat a variety of cancers, however the role of TILs in ESCC has not been substantiated with proper evidence.

Methods
The study enrolled 27 patients of ESCC between the years 2014–2019.The evaluation was based on the criteria laid down by the International TILs Working Group 2014 (recorded in percentage based on the area of stromal compartment invaded by the mononuclear inflammatory cells). Scoring was done in 400x field as follows:
Score 0- No infiltrating lymphocytes.
Score 1- Mild increase in infiltrating lymphocytes in the tumour nest or stroma.
Score 2- Increase in infiltrating lymphocytes interwoven with the tumour tissue.
Score 3- Prominent infiltrating lymphocytes incorporated in the tumour tissue.

Results
A total of 27 cases were studied, of which 17 were males (63%) and 10 were females (37%). The commonest age group was 60–70 years (12 cases- 44.4%). 22 cases had tumours sized between 3-7 cm (81.4%).
pT1–1 case (0.03%).
pT2–10 cases (37.03%).
pT3–16 cases (59.25%).
TILs were further scored based on the standard scoring system, and the results were as follows:
Score 0 in 3 cases (11.11%).
Score 1 in 14 cases (51.8%).
Score 2 in 4 cases (14.8%).
Score 3 in 6 cases (22.22%).

Conclusion
In conclusion, the commonest score of 1 was seen in 51.8% of the cases and that of score 3 was seen in 22.22% of the cases. Tumour Infiltrating Lymphocytes can hence serve as a predictor for good prognosis of Esophageal Squamous Cell Carcinoma following surgery or radiotherapy/chemotherapy.
516 THE CHARACTERIZATION OF DYSPLASIA IN BARRETT’S ESOPHAGUS—A PROSPECTIVE NATIONWIDE REGISTRY FROM THE RIBBON NETWORK
Authors: O Byrne L , O' Brien M , Muldoon C , Ryan C , Buckley M , Murphy T , Reynolds R , Patchett S , Kay E , Azam H , Robb W , Arumugasamy M , Mc Mathuna P , Leyden J , Gargan S , Doherty G , Sheahan K , Collins C , O Sullivan J , Donohoe C , Ravi N , O' Toole D , Reynolds J 
Published: September 2020

Abstract

Barrett’s Esophagus is the main pathological precursor to esophageal adenocarcinoma (EAC), dysplasia is known to be one of the principal predictors of progression to malignancy. The RIBBON Registry was established with six academic medical centers in the Republic of Ireland to identify and manage high risk Barrett’s Esophagus (BE) patients. From our database of over 4,000 patients our aim was to establish characteristics of those patients who progressed to dysplasia and furthermore to malignancy.

Methods
Data was gathered prospectively from December 2007—December 2019. Ethical approval was sought for the database at the time of establishment. Detailed endoscopic, pathological and clinical data was collected via a web-based data capture system at time of initial diagnosis and at each subsequent encounter. A data manager was appointed at each site and a national lead coordinating the project.
The Vienna Grading system was used to grade histology. Patients were included if they had an initial or subsequent diagnosis of Specialized intestinal metaplasia (SIM), Indefinite for dysplasia (IND) or Low-Grade Dysplasia (LGD).

Results
860 patients were included with a total of 3792 patient years, a male to female ratio of 2.9:1 and a median age at diagnosis of 63. 50 patients had an initial diagnosis of SIM with subsequent episodes of dysplasia while 510 patients had IND or LGD at diagnosis.
158 (18.37%) progressed to High grade dysplasia (HGD) and EAC. The overall incidence of EAC was 1.7% per year, HGD 2.4% per year and a combined rate of 4.2% per year. Median time to progression in SIM was 4.7 years, 1.1 years for IND and 9 months for LGD.

Conclusion
The overall progression of the group was much higher compared to looking at those who had SIM alone without dysplasia from the same registry (0.9% per year). Time to progression was significantly faster in the groups with initial dysplasia be that IND or LGD. In our centers those patients were followed up with repeat endoscopy as per international guidelines, the above results highlight the importance of this practice given the potential for malignancy.
534 WHICH IS THE BEST SURGICAL MANAGEMENT OF GASTROESOPHAGEAL REFLUX DISEASE (GERD) IN PATIENTS WITH SYSTEMIC SCLEROSIS WITH PULMONARY INVOLVEMENT?
Authors: Szachnowicz S , Marques F , Duarte A , Bianchi E , Nasi A , Queiroz N , Seguro F , Sallum R , Cecconello I 
Published: September 2020

Abstract

Systemic sclerosis (scleroderma) is frequently associated with both gastroesophageal reflux disease (GERD) and simultaneous esophageal dysmotility (ED). Antireflux surgery have to considerate the individual esophageal dysmotility degree of each patient. They need GERD treatment as a priority to help control worsening lung function, in patients developing pulmonary fibrosis or in lung transplantation patients. Another issue is the possibility that fundoplications in this patients can cause esophageal stasis, an event that can also disrupt lung function.

Methods
113 patients were referred for surgical treatment of GERD, related with pulmonary impairment. SS patients are the most critical, once the ED may be an obstacle to fundoplication. We divided this patients in three groups regarding the esophageal function. A- Partial fundoplication—without important affection of ED, checked by manometry, confirmed with a complete emptying of esophagus in barium swallow test. B- Laparoscopic gastric bypass for treatment of GERD (RYGBP)—aperistalsis or atonic esophageal body, with normal esophageal empty at barium test. C- Esophagectomy—Atonic esophageal body with important delayed emptying of esophagus in barium swallow test.

Results
We could follow up 4 patients in group A, 3 patients in group B and 2 patients in group C. Median follow-up was 75, 30 and 18 months for Groups A,B and C respectively. All 3 patients in the RYGB group resolved all the symptoms including heartburn and regurgitation, with a sensitive improve in lung function. Only 1 patients in the fundoplication group reported symptom improvement or resolution. The Patients at Group C have no complain of Dysphagia but referred regurgitation and difficulty feedingtill first year.

Conclusion
Laparoscopic RYGB as an anti-reflux procedure is safe and may provide an alternative to fundoplication in the treatment of GERD for systemic sclerosis patients with esophageal dysmotility. Both reflux control and dysphagia rates were improved in the RYGBP group compared with fundoplication and esophagectomy.. This finding suggests that RYGBP may be an option for the primary manage- ment of scleroderma-associated gastroesophageal reflux in patients without importnat impairing of esophageal emptying.