bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient algorithm for simulating particles in true quasiperiodic environments
Authors: Mendoza Sosa Alan Rodrigo , Kraemer Atahualpa S 
Published: April 2022

Abstract
We introduce an algorithm based on generalized dual method (GDM) to efficiently study the dynamics of a particle in quasiperiodic environments without the need to use periodic approximations or to save the information of the vertices that make up the quasiperiodic lattice. We show that the computation time and the memory required to find the tile in which a particle is located as a function of the distance R to the center of symmetry remains constant in our algorithm, while using the GDM directly both quantities go like R
2. This allows us to perform realistic simulations with low consumption of computational resources. The algorithm can be used to study any quasiperiodic lattice that can be produced by the cut-and-project method. Using this algorithm, we have calculated the free path length distribution in quasiperiodic Lorentz gases reproducing previous results and for systems with high symmetries at the Boltzmann–Grad limit. We have found for the Boltzmann–Grad limit, that the distribution of free paths depends on the rank r of the quasiperiodic system and not on its symmetry. The distribution as a function of the free path length l appears to be a combination of exponential decay and a power-law behavior. The latter seems to become important only for probabilities less than

(

2

r
−
2

r

(

r
+
1

)

)

−
1

, showing an exponential decaying free-path length distribution for r → ∞, similar to what is observed in disordered systems.
Number of distinct sites visited by a resetting random walker
Authors: Biroli Marco , Mori Francesco , Majumdar Satya N 
Published: April 2022

Abstract
We investigate the number V

p
(n) of distinct sites visited by an n-step resetting random walker on a d-dimensional hypercubic lattice with resetting probability p. In the case p = 0, we recover the well-known result that the average number of distinct sites grows for large n as ⟨V
0(n)⟩ ∼ n

d/2 for d < 2 and as ⟨V
0(n)⟩ ∼ n for d > 2. For p > 0, we show that ⟨V

p
(n)⟩ grows extremely slowly as

∼

log

(

n

)

d

. We observe that the recurrence-transience transition at d = 2 for standard random walks (without resetting) disappears in the presence of resetting. In the limit p → 0, we compute the exact crossover scaling function between the two regimes. In the one-dimensional case, we derive analytically the full distribution of V

p
(n) in the limit of large n. Moreover, for a one-dimensional random walker, we introduce a new observable, which we call imbalance, that measures how much the visited region is symmetric around the starting position. We analytically compute the full distribution of the imbalance both for p = 0 and for p > 0. Our theoretical results are verified by extensive numerical simulations.
Cartilage tissue engineering by extrusion bioprinting utilizing porous hyaluronic acid microgel bioinks
Authors: Flégeau Killian , Puiggali-Jou Anna , Zenobi-Wong Marcy 
Published: April 2022

Abstract
3D bioprinting offers an excellent opportunity to provide tissue-engineered cartilage to microtia patients. However, hydrogel-based bioinks are hindered by their dense and cell-restrictive environment, impairing tissue development and ultimately leading to mechanical failure of large scaffolds in vivo. Granular hydrogels, made of annealed microgels, offer a superior alternative to conventional bioinks, with their improved porosity and modularity. We have evaluated the ability of enzymatically crosslinked hyaluronic acid (HA) microgel bioinks to form mature cartilage in vivo. Microgel bioinks were formed by mechanically sizing bulk HA-tyramine hydrogels through meshes with aperture diameters of 40, 100 or 500 µm. Annealing of the microgels was achieved by crosslinking residual tyramines. Secondary crosslinked scaffolds were stable in solution and showed tunable porosity from 9% to 21%. Bioinks showed excellent rheological properties and were used to print different objects. Printing precision was found to be directly correlated to microgel size. As a proof of concept, freeform reversible embedding of suspended hydrogels printing with gelation triggered directly in the bath was performed to demonstrate the versatility of the method. The granular hydrogels support the homogeneous development of mature cartilage-like tissues in vitro with mechanical stiffening up to 200 kPa after 63 d. After 6 weeks of in vivo implantation, small-diameter microgels formed stable constructs with low immunogenicity and continuous tissue maturation. Conversely, increasing the microgel size resulted in increased inflammatory response, with limited stability in vivo. This study reports the development of new microgel bioinks for cartilage tissue biofabrication and offers insights into the foreign body reaction towards porous scaffolds implantation.
Effect of lens-to-sample distance on spatial uniformity and emission spectrum of flat-top laser-induced plasma
Authors: FU Hongbo , WANG Huadong , ZHANG Mengyang , WU Bian , ZHANG Zhirong 
Published: April 2022

Abstract
The optimal spectral excitation and acquisition scheme is explored by studying the effect of the lens-to-sample distance (LTSD) on the spatial homogeneity and emission spectra of flat-top laser converging spot induced plasma. The energy distribution characteristics before and after the convergence of the laser beam with quasi flat-top intensity profile used in this study are theoretically simulated and experimentally measured. For an aspheric converging mirror with a focal length of 100 mm, the LTSD (106 mm ≥ LTSD ≥ 96 mm) was changed by raising the stainless-steel sample height. The plasma images acquired by ICCD show that there is air breakdown when the sample is below the focal point, and a ring-like plasma is produced when the sample is above the focal point. When the sample is located near the focal point, the plasma shape resembles a hemisphere. Since the spectral acquisition region is confined to the plasma core and the image contains all the optical information of the plasma, it has a lower relative standard deviation (RSD) than the spectral lines. When the sample surface is slightly higher than the focal plane of the lens, the converging spot has a quasi flat-top distribution, the spatial distribution of the plasma is more uniform, and the spectral signal is more stable. Simultaneously, there is little difference between the RSD of the plasma image and the laser energy. In order to further improve the stability of the spectral signal, it is necessary to expand the spectral acquisition area.
Electronic and interfacial properties of graphene/HfS2 van der Waals heterostructure
Authors: Karbasizadeh S , Fanaeeparvar F , Abdolhosseini Sarsari I 
Published: April 2022

Abstract
Using density functional theory calculations and the addition of van der Waals correction, the graphene/HfS2 heterojunction is constructed, and its electronic properties are examined thoroughly. This interface is determined as n-type ohmic, and the impacts of different amounts of interlayer distance and strain on the contact are shown using Schottky barrier height and electron injection efficiency. Dipole moment and work function of the interface are also altered when subjected to change in these two categories. The effects of an applied electric field on transforming the ohmic contact to Schottky is also investigated. The conclusions given can assist in the design and modeling of HfS2 based devices in the future.
MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach
Authors: Ding Hongyu , Luo Junwei 
Published: April 2022

Abstract
Structural variations (SVs) play important roles in human genetic diversity; deletions and insertions are two common types of SVs that have been proven to be associated with genetic diseases. Hence, accurately detecting and genotyping SVs is significant for disease research. Despite the fact that long-read sequencing technologies have improved the field of SV detection and genotyping, there are still some challenges that prevent satisfactory results from being obtained. In this paper, we propose MAMnet, a fast and scalable SV detection and genotyping method based on long reads and a combination of convolutional neural network and long short-term network. MAMnet uses a deep neural network to implement sensitive SV detection with a novel prediction strategy. On real long-read sequencing datasets, we demonstrate that MAMnet outperforms Sniffles, SVIM, cuteSV and PBSV in terms of their F1 scores while achieving better scaling performance. The source code is available from https://github.com/micahvista/MAMnet.
The prediction approach of drug-induced liver injury: response to the issues of reproducible science of artificial intelligence in real-world applications
Authors: Chen Zhao , Jiang Yin , Zhang Xiaoyu , Zheng Rui , Qiu Ruijin , Sun Yang , Zhao Chen , Shang Hongcai 
Published: April 2022

Abstract
In the previous study, we developed the generalized drug-induced liver injury (DILI) prediction model—ResNet18DNN to predict DILI based on multi-source combined DILI dataset and achieved better performance than that of previously published described DILI prediction models. Recently, we were honored to receive the invitation from the editor to response the Letter to Editor by Liu Zhichao, et al. We were glad that our research has attracted the attention of Liu’s team and they has put forward their opinions on our research. In this response to Letter to the Editor, we will respond to these comments.
Current understanding in deciphering trophoblast cell differentiation during human placentation
Authors: Li Qian , Wu Hao , Wang Yue , Wang Hongmei 
Published: April 2022

AbstractThe placenta is a unique organ that forms during gestation and supports fetus survival and communication with the mother. However, of such an essential organ for a successful pregnancy, our knowledge is limited. New progress has been made for human placenta study in recent years. We herein summarize the current understanding of human placental trophoblast differentiation and the molecules that govern trophoblast cell lineage specification. More importantly, the powerful tools for placental studies are also described such as human trophoblast stem cells, 3-dimensional (3D) trophoblast organoids, engineering-based placental devices, and single-cell RNA sequencing. These advances have brought us new insights into placental development and provided multiple investigation strategies for deciphering molecular mechanisms.
Cryptic speciation shapes the biogeographic history of a northern distributed moss
Authors: Escolástico-Ortiz Dennis Alejandro , Hedenäs Lars , Quandt Dietmar , Harpke Dörte , Larraín Juan , Stech Michael , Villarreal A Juan Carlos 
Published: April 2022

Abstract
Increasing evidence indicates that wide distributed bryophyte taxa with homogeneous morphology may represent separate evolutionary lineages. The evolutionary histories of these cryptic lineages may be related to historical factors, such as the climatic oscillations in the Quaternary. Thus, the post-glacial demographic signatures paired with cryptic speciation may result in complex phylogeographic patterns. This research has two aims: to determine whether the widespread moss Racomitrium lanuginosum represents cryptic molecular taxa across the Northern Hemisphere and to infer the effects of Quaternary glaciations on spatial genetic diversity. We used the internal transcribed spacer (ITS) marker to resolve the phylogeographic history of the species and single nucleotide polymorphisms (genotyping-by-sequencing) to infer the genetic structure and demographic history. Finally, we assessed the historical changes in the distribution range using species distribution models. Racomitrium lanuginosum comprises distinct molecular lineages sympatrically distributed in the Northern Hemisphere. We also uncovered long-distance dispersal from eastern North America to Scandinavia and potential in situ survival in northern Scandinavia. Due to the genetic signatures, the Alaska Peninsula could be considered a glacial refugium. The species experienced post-glacial expansion northwards in the Northern Hemisphere, mainly from the Alaska Peninsula. Our results exemplify the complex phylogeographic history in cold environments and contribute to recognizing evolutionary patterns in the Northern Hemisphere.
The clinical, molecular, and therapeutic features of patients with IL10/IL10R deficiency: a systematic review
Authors: Sharifinejad Niusha , Zaki-Dizaji Majid , Sepahvandi Roya , Fayyaz Farimah , dos Santos Vilela Maria Marluce , ElGhazali Gehad , Abolhassani Hassan , Ochs Hans D , Azizi Gholamreza 
Published: April 2022

Abstract
Interleukin10 (IL10) and IL10 receptor (IL10R) deficiencies are monogenic inborn errors of immunity (IEI) causing early-onset inflammatory bowel diseases (IBD). In this report, we systematically reviewed articles that included related keywords using PubMed, Web of Science, and Scopus databases. The articles were screened for eligibility criteria before data extraction. We assessed 286 patients (44.5% female) with IL10 and/or IL10R deficiencies who were predominantly from China (40.7%), Italy (13.9%), and South Korea (8.5%). The median age of onset was 1.0 (0.3–4.0) months with a median age of genetic diagnosis at 16.0 (7.4–81.0) months. Consanguinity was reported in all evaluable patients with IL10 deficiency and in 38.2% of patients with IL10R deficiency (22.9% of patients with IL10RA, and 79.4% of patients with IL10RB deficiency). The most prevalent mutations in IL10RA were c.301C&gt;T (p.R101W) and c.537G&gt;A (p.T179T), those in IL10RB were c.139A&gt;G (p.K47E) and c.611G&gt;A (p.W204X). Auto-inflammation and enteropathy were present in all cases. The first presentation of both groups was protracted diarrhea (45.7%), bloody diarrhea (17.8%), and colitis (15.5%). Patients with IL10R deficiency had a high frequency of dermatologic manifestations (50.5%) and failure to thrive (60.5%), while IL10-deficient patients lacked those complications. In the majority of patients, the basic immunologic parameters were in normal ranges. Of the entire publications, 30.7% underwent hemopoietic stem cell transplantation, 57.5% surgery, and 86.6% immunosuppressive treatment. The 10-year survival rate was higher in patients with IL10 deficiency than in patients with IL10R deficiency. In conclusion, IL10/IL10R deficiency predominantly presents with treatment-resistant, early-onset IBD within the first months of life. We detected no clear correlation between the phenotype of patients carrying the same variant. The high prevalence of distinct clinical manifestations reported in IL10RA- and IL10RB-deficient patients might be attributable to the interactions between the target tissue and cytokines other than IL10 capable of binding to IL10RB. These results gain translational significance by contributing to earlier diagnosis, adequate therapy, and avoiding delay in the diagnosis and unfavorable outcomes.
Supporting the Art: Medication Adherence Patterns in Persons Prescribed Ingestible Sensor-enabled Oral Pre-Exposure Prophylaxis to Prevent Human Immunodeficiency Virus Infection
Authors: Browne Sara H , Vaida Florin , Umlauf Anya , Tucker Amanda J , Blaschke Terrence F , Benson Constance A 
Published: April 2022

Abstract

Background
Timely, accurate adherence data may support oral pre-exposure prophylaxis (PrEP) success and inform prophylaxis choice. We evaluated a Food and Drug Administration (FDA)-approved digital health feedback system (DHFS) with ingestible-sensor-enabled (IS) tenofovir-disoproxil-fumarate plus emtricitabine (Truvada®) in persons starting oral PrEP.

Methods
Human immunodeficiency virus (HIV)-negative adults were prescribed IS-Truvada® with DHFS for 12 weeks to observe medication taking behavior. Baseline demographics, urine toxicology, and self-report questionnaires were obtained. Positive detection accuracy and adverse events were computed as percentages, with Kaplan Meier Estimate for persistence-of-use. In participants persisting ≥28 days, adherence patterns (taking and timing) were analyzed, and mixed-effects logistic regression modeled characteristics associated with treatment adherence.

Results
Seventy-one participants were enrolled, mean age 37.6 years (range 18–69), 90.1% male, 77.5% White, 33.8% Hispanic, 95.8% housed, and 74.6% employed. Sixty-three participants (88.7%) persisted ≥28 days, generating 4987 observation days, average 79.2 (29–105). Total confirmed doses were 86.2% (95% confidence interval [CI] 82.5, 89.4), decreasing over time, odds ratio (OR) 0.899 (95% CI .876, .923) per week, P &lt; .001; 79.4% (95% CI 66.7%, 87.3%) of participants had ≥80% adherence. Pattern analysis showed days without confirmed doses clustered (P = .003); regular dose timing was higher among participants with ≥80% confirmed doses (0.828, 95% CI .796 to .859) than among those with &lt;80% (0.542, 95% CI95 .405 to .679) P &lt; .001. In multi-predictor models, better adherence was associated with older age, OR 1.060 (95% CI 1.033, 1.091) per year, P &lt; .001; negative vs positive methamphetamine screen, OR 5.051 (95% CI 2.252, 11.494), P &lt; .001.

Conclusions
DHFS with IS-Truvada® distinguished adherent persons from those potentially at risk of prophylactic failure. Ongoing methamphetamine substance use may impact oral PrEP success.
Safety and Efficacy of an AIEC-targeted Bacteriophage Cocktail in a Mice Colitis Model
Authors: Titécat Marie , Rousseaux Christel , Dubuquoy Caroline , Foligné Benoît , Rahmouni Oumaïra , Mahieux Séverine , Desreumaux Pierre , Woolston Joelle , Sulakvelidze Alexander , Wannerberger Kristin , Neut Christel 
Published: April 2022

Abstract

Background and aims
Adherent invasive Escherichia coli [AIEC] are recovered with a high frequency from the gut mucosa of Crohn’s disease patients and are believed to contribute to the dysbiosis and pathogenesis of this inflammatory bowel disease. In this context, bacteriophage therapy has been proposed for specifically targeting AIEC in the human gut with no deleterious impact on the commensal microbiota.

Methods
The in vitro efficacy and specificity of a seven lytic phage cocktail [EcoActive™] was assessed against [i] 210 clinical AIEC strains, and [ii] 43 non-E. coli strains belonging to the top 12 most common bacterial genera typically associated with a healthy human microbiome. These data were supported by in vivo safety and efficacy assays conducted on healthy and AIEC-colonized mice, respectively.

Results
The EcoActive cocktail was effective in vitro against 95% of the AIEC strains and did not lyse any of the 43 non-E. coli commensal strains, in contrast to conventional antibiotics. Long-term administration of the EcoActive cocktail to healthy mice was safe and did not induce dysbiosis according to metagenomic data. Using a murine model of induced colitis of animals infected with the AIEC strain LF82, we found that a single administration of the cocktail failed to alleviate inflammatory symptoms, while mice receiving the cocktail twice a day for 15 days were protected from clinical and microscopical manifestations of inflammation.

Conclusions
Collectively, the data support the approach of AIEC-targeted phage therapy as safe and effective treatment for reducing AIEC levels in the gut of IBD patients.
Assessment of the systolic rise time by photoplethysmography in peripheral arterial diseases: a comparative study with ultrasound Doppler
Authors: Amrani Samantha , Eveilleau Kornelia , Fassbender Verena , Obeid Hasan , Abi-Nasr Imad , Giordana Pascal , Hallab Magid , Leftheriotis Georges 
Published: April 2022

Abstract

Aims
Peripheral arterial disease (PAD) is a major public health burden requiring more intensive population screening. Ankle brachial index (ABI) using arm and ankle cuffs is considered as the reference method for the detection of PAD. Although it requires a rigorous methodology by trained operators, it remains time-consuming and more technically difficult in patients with diabetes due to mediacalcosis. Techniques based on the study of hemodynamic, such as the systolic rise time (SRT), appear promising but need to be validated. We retrospectively compared the reliability and accuracy of SRT using a photoplethysmography (PPG) technique to the SRT measured by ultrasound doppler (UD) in PAD patients diagnosed with the ABI (137 patients, 200 lower limbs).

Methods and results
There was a significant correlation between SRT measured with UD (SRTud) compared with that with PPG (SRTppg, r = 0.25; P = 0.001). Best correlation was found in patients without diabetes (r = 0.40; P = 0.001). Bland and Altman analysis showed a good agreement between the SRTud and SRTppg. In contrast, there was no significant correlation between UD and PPG in diabetes patients. Furthermore, patients with diabetes exhibited a significant increase of SRTppg (P = 0.02) compared with patients without diabates but not with the SRTud (P = 0.18). The SRTppg was significantly linked to the arterial velocity waveforms, the type of arterial lesion but not vascular surgery revascularization technique.

Conclusion
This monocentric pilot study shows that SRT measured with the PPG signal reliably correlates with SRT recorded with UD. The PPG is an easy to use technique in the hand of non-expert with a potential interest for general screening of PAD, especially in diabetes patients, due to its ease to use.
Sex differences in temporal trends in main and secondary pulmonary embolism diagnosis and case fatality rates: 2003–2019
Authors: Vicent Lourdes , Martín de la Mota Sanz David , Rosillo Nicolás , Peñaloza-Martínez Eduardo , Moreno Guillermo , Bernal José Luis , Elola Javier , Bueno Héctor 
Published: April 2022

AbstractAimsThere is controversy regarding the incidence and outcomes of pulmonary embolism (PE) according to sex. Our aim was to address sex differences in temporal trends in main and secondary hospital PE diagnoses, management and case fatality rates (CFR).Methods and resultsRetrospective analysis of Spain´s National Healthcare System hospital database, years 2003–2019, for patients ≥18 years with main or secondary PE diagnosis. Trends by sex in hospital diagnosis, use of procedures, and CFRs were analysed by joinpoint and Poisson regression models. Of 339 469 PE diagnoses, 52% were in women. Sixty-five percent were main diagnosis, 35.2% secondary. Total annual diagnoses and frequentation rates increased similarly in men and women: average annual percent change (AAPC): 2.0% (95% CI, 1.3–2.6; P &lt; 0.005). Secondary PEs were more common in men (37.8% vs. 32.9%, P &lt; 0.001). Men showed greater comorbidity than women (Charlson index 2.22 ± 0.01 vs. 1.74 ± 0.01, P &lt; 0.001), particularly cancer in the secondary diagnosis group (40.9% vs. 31.6%, P &lt; 0.001). CFRs for PE as main diagnosis were comparable and decreased in parallel in men (from 13.8% in 2003 to 7.3% in 2019) and women (from 13.1% in 2003 to 6.9% in 2019). However, for PE as secondary diagnosis, CFRs remained higher (P &lt; 0.001) in men (from 42.5% in 2003 to 26.2% in 2019) than women (from 34.4% in 2003 to 22.8% in 2019).ConclusionPE hospital diagnosis increased significantly between 2003 and 2019 in men and women for both main and secondary diagnosis. Although in-hospital CFR decreased one third still remains very high, especially in men with secondary PE diagnosis.