bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffusion in a partially absorbing medium with position and occupation time resetting
Authors: Bressloff Paul C 
Published: June 2022

AbstractIn this paper we consider diffusion in a domain Ω containing a partially absorbing targetMwith position and occupation time resetting. The occupation timeAtis a Brownian functional that determines the amount of time that the particle spends inMover the time interval [0,t]. We assume that there exists some internal stateUtof the particle at timetwhich is modified whenever the particle is diffusing withinM. The stateUtis taken to be a monotonically increasing function ofAt, and absorption occurs as soon asUtcrosses some fixed threshold. We first show how to analyze threshold absorption in terms of the joint probability density or generalized propagatorP(x,a,t|x0) for the pair (Xt,At) in the case of a non-absorbing substrateM, whereXtis the particle position at timetandx0is the initial position. We then introduce a generalized stochastic resetting protocol in which both the positionXtand the internal stateUtare reset to their initial values,Xt→x0andUt→0, at a Poisson rater. The latter is mathematically equivalent to resetting the occupation time,At→ 0. Since resetting is governed by a renewal process, the survival probability with resetting can be expressed in terms of the survival probability without resetting, which means that the statistics of absorption can be determined by calculating the double Laplace transform ofP(x,a,t|x0) with respect totanda. In order to develop the basic theory, we focus on one-dimensional diffusion withMgiven by a finite or semi-infinite interval, and explore how the mean first passage time with resetting depends on various model parameters. We also compare the threshold mechanism with the classical case of a constant absorption rate.
Effects of nitrogen and phosphorus on chlorophyll a in lakes of China: a meta-analysis
Authors: Yu Guanghui , Zhang Shanhong , Qin Wei , Guo Yu , Zhao Ran , Liu Chunhong , Wang Chengguo , Li Daoliang , Wang Yang 
Published: June 2022

Abstract
Whether or not chlorophyll a (Chla) is limited by nitrogen (N) or phosphorus (P), or both, remains highly debated. In part this is due to the lack of a robust statistical rarely considered using a statistical method in studies of peer-review research of lakes. Individual studies only used the use of the relationship between Chla and nutrients to judge the effects of N and P, ignoring the spatial heterogeneity of the ecological environment. Here, we evaluated the effects of nitrogen and phosphorus on Chla via a meta-analysis. The dataset consists of 1024 observations from 34 lakes in China. The results show that Chla is one of the most important indicators of water eutrophication, both nutrients were related Chla trophic state, and that TP plays an important role over TN, especially in the hypereutrophic Chla conditions. With the increase of TN/TP, Chla concentration is decreased, which may be the co-limited of TN and TP. These three values largely explained the increment of eutrophication Chla, although the relative effects differed across nutrients, with changes in the TN total contributing 5.2% of the increment in Chla, while the TP change contributed 272.0% of the increment in Chla. At spatial scales, logarithm-transformed response ratio (

ln
R
R

) of Chla indicated that the lake shifts from N limitation (64.0% > 28.0%) in oligo-mesotrophic to P limitation (170.0% > 99.0%) in eutrophic and co-limitation (66.0% and 46.0%) by N & P in hypereutrophic. These results demonstrate that TP reduction can mitigate eutrophication in most large lakes but a dual TN and TP reduction may be needed in eutrophic lakes, especially in hypereutrophic states. This study highlights the differential effects of the three factors concentration, which may offer important implications for better management of the response of the eutrophication lakes to nutrients (N and P) in the future.
Nasal nitric oxide is decreased in acute mild COVID-19 and related to viral load
Authors: Tamminen Pekka J , Kerimov Dominik M , Viskari Hanna , Aittoniemi Janne , Syrjänen Jaana , Lehtimäki Lauri 
Published: June 2022

Abstract
Gaseous nitric oxide levels from the lungs (FeNO) and from the nose (nNO) have been demonstrated to react to acute infection or influenza vaccination. There are no published data on nNO levels during acute COVID-19, but normal levels of FeNO have been reported in one study. Our aim was to assess if acute mild COVID-19 alters nasal or bronchial NO output at the time of acute infection and at a two-month follow up, and if this is related to symptoms or viral load. This study included 82 subjects with mild acute airway infection who did not need hospitalization: 43 cases (reverse transcription polymerase chain reaction (RT-PCR)-positive for SARS-CoV-2 in routine testing from nasopharynx) and 39 age- (±5 years) and gender-matched controls (RT-PCR-negative for SARS-CoV-2). During acute infection, the cases had lower nNO compared to controls (158 [104–206] vs. 232 [203–279] nl min−1; p < 0.001), but after two months, there was no significant difference between the groups (230 [179–290] vs. 268 [222–320] nl min−1; p = 0.162). There was no difference in FeNO between the groups at either of the visits. Nasal NO correlated with the cycle threshold (Ct) value of the nasopharyngeal RT-PCR test for SARS-CoV-2 (Spearman’s r
s = 0.550; p < 0.001), that is, nNO was lower with a higher viral load. Nasal NO output was decreased in acute COVID-19 in relation to higher viral load, suggesting that the type and intensity of inflammatory response affects the release of NO from airway mucosa. In these subjects without significant lower airway involvement, there were no clinically relevant findings regarding FeNO.
Strategically designed SPEEK nanofibrous scaffold with tailored delivery of resveratrol for skin wound regeneration
Authors: Ekambaram Rajalakshmi , Saravanan Saisupriyalakshmi , Dharmalingam Sangeetha 
Published: June 2022

Abstract
Electro-spinnable polymeric materials can easily form two-dimensional (2D) nanofibrous scaffolds improving biochemical functionalities specially in the area of skin wound healing and nanomedicine, but it has been hard to achieve this on a highly mechanically stable biopolymer, Poly ether ether ketone (PEEK), due to its intrinsic hydrophobicity and chemical inertness. Herein, we demonstrated a novel nanomedicine healing system consisting of sulphonated poly ether ether ketone combined with resveratrol (SPEEK + RSV), which could act as an effective 2D nano bio-material in vitro and in vivo, without observable cytotoxicity. The fabricated nanocomposites exhibited enriched skin cell proliferation and adhesion as confirmed from the results of MTT, cell adhesion and live-dead assay. Results of SEM analysis showed a uniform nano-sized distribution with adequate pore size and porosity % facilitating a desired breathable environment at the wound site. The results of FT-IR, tensile studies and TGA analyses confirmed the presence of appropriate bonds and improved mechanical stability of the RSV incorporated nanofibrous scaffold. Results of anti-microbial analysis portrayed good potentiality of the fabricated nanofibers in treating wounds colonized with bacterial infections. Controlled drug release of resveratrol established the bio-compatibility of the nanofibers in skin wound regeneration. In vivo analysis assessed in female Wistar rats enabled complete wound closure with 100% wound contraction within 16 days. Results of histopathology analysis through H-E and MT staining presented the re-surfing of the wound environment with regeneration of epithelium, granulation tissue and collagen. Thus, the fabricated 2D nanofibrous scaffold incorporated with pharmaceutical RSV bio-medicine perceptively mimicked skin ECM convincingly aiding the progression of skin wound regeneration mechanism.
Emulating atmospheric turbulence effects on a micro-mirror array: assessing the DMD for use with free-space-to-fibre optical connections
Authors: Benton David M , Ellis Andrew D , Li Yiming , Hu Zhouyi 
Published: June 2022

Abstract
Emulated atmospheric turbulence effects constructed from a set of 22 Zernike modes have been written upon a DMD micromirror array operating as a binary amplitude spatial light modulator. Sequences of aberrated frames with controlled amounts of turbulence have been produced and can be operated at controlled rates that can exceed 1 kHz rates which can be seen in strong turbulence. In this case 400 Hz was chosen and the scintillation levels observed for the same turbulence sequence with single, few and multi-mode fibres at a receiver. Resulting scintillation levels are consistent with standard turbulence models. Increased received intensity and reduced scintillation was observed with larger core fibres and related to aberration-induced focal spot size. Correlation between the received intensity variation and the amplitude variations for individual Zernike modes demonstrates specifically the effect of atmospheric induced beam wander when focusing into a receive fibre. The DMD is thus shown to be able to generate both the necessary frequency content and range of scintillation required for atmospheric emulation.
Emergence of wandering stable components
Authors: Berger Pierre , Biebler Sébastien 
Published: June 2022

We prove the existence of a locally dense set of real polynomial automorphisms of

C

2

\mathbb C^2

displaying a wandering Fatou component; in particular this solves the problem of their existence, reported by Bedford and Smillie in 1991. These Fatou components have non-empty real trace and their statistical behavior is historic with high emergence. The proof is based on a geometric model for parameter families of surface real mappings. At a dense set of parameters, we show that the dynamics of the model displays a historic, high emergent, stable domain. We show that this model can be embedded into families of Hénon maps of explicit degree and also in an open and dense set of

5
5

-parameter

C
r

C^r

-families of surface diffeomorphisms in the Newhouse domain, for every

2
≤
r
≤
∞

2\le r\le \infty

and

r
=
ω

r=\omega

. This implies a complement of the work of Kiriki and Soma [Adv. Math. 306 (2017), pp. 524–588], a proof of the last Taken’s problem in the

C

∞

C^{\infty }

and

C
ω

C^\omega

-case. The main difficulty is that here perturbations are done only along finite-dimensional parameter families. The proof is based on the multi-renormalization introduced by Berger [Zoology in the Hénon family: twin babies and Milnor’s swallows, 2018].
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data
Authors: Ullah Matee , Hadi Fazal , Song Jiangning , Yu Dong-Jun 
Published: June 2022

AbstractMotivationCharacterization of protein subcellular localization has become an important and long-standing task in bioinformatics and computational biology, which provides valuable information for elucidating various cellular functions of proteins and guiding drug design.ResultsHere, we develop a novel bioimage-based computational approach, termed PScL-DDCFPred, to accurately predict protein subcellular localizations in human tissues. PScL-DDCFPred first extracts multiview image features, including global and local features, as base or pure features; next, it applies a new integrative feature selection method based on stepwise discriminant analysis and generalized discriminant analysis to identify the optimal feature sets from the extracted pure features; Finally, a classifier based on deep neural network (DNN) and deep-cascade forest (DCF) is established. Stringent 10-fold cross-validation tests on the new protein subcellular localization training dataset, constructed from the human protein atlas databank, illustrates that PScL-DDCFPred achieves a better performance than several existing state-of-the-art methods. Moreover, the independent test set further illustrates the generalization capability and superiority of PScL-DDCFPred over existing predictors. In-depth analysis shows that the excellent performance of PScL-DDCFPred can be attributed to three critical factors, namely the effective combination of the DNN and DCF models, complementarity of global and local features, and use of the optimal feature sets selected by the integrative feature selection algorithm.Availability and implementationhttps://github.com/csbio-njust-edu/PScL-DDCFPred.Supplementary informationSupplementary data are available at Bioinformatics online.
Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families
Authors: Fukunaga Tsukasa , Iwasaki Wataru 
Published: June 2022

AbstractSummaryWe present Mirage 2.0, which accurately estimates gene-content evolutionary history by considering heterogeneous evolutionary patterns among gene families. Notably, we introduce a deterministic pattern mixture model, which makes Mirage substantially faster and more memory-efficient to be applicable to large datasets with thousands of genomes.Availability and implementationThe source code is freely available at https://github.com/fukunagatsu/Mirage.Supplementary informationSupplementary data are available at Bioinformatics online.
HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements
Authors: Singh Vinod Kumar , Misra Rohan , Almo Steven C , Steidl Ulrich G , Bülow Hannes E , Zheng Deyou 
Published: June 2022

AbstractSummaryThe functional sub-string(s) of a biopolymer sequence defines the specificity of its interaction with other biomolecules and is often referred to as motifs. Computational algorithms and software have been broadly developed for finding such motifs in sequences in which the individual elements are single characters, such as those in DNA and protein sequences. However, there are more complex scenarios where the motifs exist in non-single-letter contexts, e.g. preferred patterns of chemical modifications on proteins, DNAs, RNAs or polysaccharides. To search for those motifs, we describe a new method that converts the modified sequence elements to representative single-letter codes and then uses a modified Gibbs-sampling algorithm to define the position specific scoring matrix representing the motif(s). As a proof of principle, we describe the implementation and application of an R package for discovering heparan sulfate (HS) motifs in glycan sequences, which are important in regulating protein–protein interactions. This software can be valuable for analyzing high-throughput glycoprotein binding data using microarrays with HS oligosaccharides or other biological polymers.Availability and implementationHSMotifDiscover is freely available as an open source R package released under an MIT license at https://github.com/bioinfoDZ/HSMotifDiscover and also available in the form of an app at https://hsmotifdiscover.shinyapps.io/HSMotifDiscover_ShinyApp/.Supplementary informationSupplementary data are available at Bioinformatics online.
O-023 A randomized control trial on the effect of intrauterine HCG flushing on reproductive outcomes
Authors: Gedela D R , Mantravadi K , Sundari S 
Published: June 2022

Abstract

Study question
Can Intra Uterine Flushing with Human Chorionic Gonadotropin (hCG) optimize embryo implantation and reproductive outcomes in Assisted Reproductive Technique(ART) cycles?

Summary answer
Uterine flushing with hCG does not seem to enhance embryo implantation and optimize reproductive outcomes

What is known already
Human Chorionic Gonadotropin (hCG) hormone has shown to play an important role in embryo implantation. Role of hCG flushing to uterine cavity has been proposed as one of the interventions to optimize embryo implantation, but its efficiency has been debatable.

Study design, size, duration
This study is a Randomised Control trial (RCT) with prior approval from Institution Ethical Review Board(IEC Ref. No. ECR/1312/inst/tg/2019). Study duration between November 2020-November 2021 at a private clinic. Women undergoing In-Vitro fertilization (IVF) cycles were randomised to no hCG flush group (n = 80) and hCG flush group (n = 100). Women &gt;37yrs age and BMI &gt;30 or having some uterine pathology or willing for Pre-Implantation Genetic Testing (PGT) or donor gamete cycles were excluded from this study

Participants/materials, setting, methods
Women recruited in this study underwent ovarian stimulation as per the institutes standard operating protocols (SOP). All embryos subjected to blastocyst culture and freeze all strategy followed. In a frozen embryo replacement cycle two good grade blastocysts were transferred. In hCG flush group, 48-72hrs before anticipated embryos transfer (ET) 500IU of commercially available hCG hormone was instilled into the uterine cavity. No hCG Flush group did not have any intervention

Main results and the role of chance
Clinical Pregnancy rates (CPR), Implantation Rates (IR), Multiple Pregnancy rates (MPR) were compared between the groups.

Means of Reproductive outcomes between hCG Vs no hCG group were as follows
CPR – 71% Vs 76% (p = 0.45) IR – 59% Vs 55%(p=0.59)MPR – 18% Vs 25%(p=0.25) Data from this RCT shows that hCG flush does not seem to enhance embryo implantation. Role of hCG flush to optimize reproductive outcomes is questionable.

Limitations, reasons for caution
This study has not evaluated the miscarriage rates and live birth rates

Wider implications of the findings
Ways to enhance embryo implantation and optimising reproductive outcomes still needs further research. hCG flushing might not be a beneficial intervention to optimise embryo implantation. However, a subgroup analysis to identify efficiency of hCG in a particular group of patients like thin endometrium could be further explored.

Trial registration number
NA
O-046 Reproductive prospects for ICSI children
Authors: Belva F , Hes F , Tournaye H , Bonduelle M , Liebaers I , Verheyen G , Van Steirteghem A 
Published: June 2022

Abstract
Intracytoplasmic sperm injection (ICSI), developed 30 years ago in our Center, allowed men with low to extremely low sperm quality to become the genetic father of their child. Overall, ICSI is now applied in up to 70% of all ART cycles and has resulted in the birth of millions of children worldwide.
ICSI circumvents natural sperm selection mechanisms and concerns related to transgenerational inheritance of male infertility following ICSI could not be fully answered till today, given the young age of the offspring born after ICSI. Since genetic abnormalities account for one third of all cases of male factor infertility, it is essential to identify these genetic abnormalities because of the potential risk of their transmission to the offspring through the use of ART. As ICSI is nowadays performed even in couples with normal semen parameters, the disentanglement of procedure-related and parental background-related factors on the health of the offspring is important.
Due to the safety concerns regarding the health of children born after ART, a longitudinal follow-up program was set up in our Center in the 80’s, resulting in data of more than 50 000 pregnancies. To date, more than 25 000 children are conceived after ICSI in our Center. We have not only the worldwide eldest cohort of ICSI offspring but also a uniform cohort of children and young adults conceived by ICSI because of (severe) male factor infertility.
We present the results of these prospective studies with focus on the reproductive health in ICSI children between 8 and 22 years and compare these with available data from others. First of all, we will show data on the gonadal function assessed both clinically and by means of biomarkers at pre-pubertal and pubertal ages in ICSI boys. Secondly, we will present findings on the reproductive status of young adult men and women conceived after ICSI between 1992 and 1996: results of hormonal work-up, physical examination and semen parameters for ICSI men and results of hormone levels and antral follicle counts for ICSI women.
Finally, we will discuss the findings in these cohorts of children and young adults conceived because of male infertility in view of the available literature regarding reproductive function in offspring conceived following ICSI.
O-056 The duty to do no harm implies that some requests for treatment should be denied
Authors: Mol B W 
Published: June 2022

Abstract
One unique character of reproductive medicine is the involvement of multiple individuals. Apart from individual(s) who want to become parents, also the interests offspring that is created by reproductive medicine treatments should be considered. This unique character brings unique ethical challenges, as the principle ‘Primum non nocere’ should be applied on all involved, including the children born form fertility treatments. I will present a framework that involves three dimensions, the risks for the mother, risks for the offspring and consequences for society and the public system.
First, treatment can be refused as there is uncertainty about the quality of life of the future offspring. I will argue that before the treatment is started, the new individual is not there and cannot claim any rights. The care provider has a responsibility towards the future individual, not only in terms of health, but also from a social perspective. If the future child going to live an abusive family, it might be better of not existing.
Second, treatment can be refused because of an unhealthy lifestyle or a health risk for the future mother. Treatment might be refused because a mother has an underlying disease that could severely exacerbate during pregnancy, or because she smokes or is obese. I will argue that in these situations decisions should be made in the context of absolute health risks for the mother and the offspring, as well as success rates of treatments. I will demonstrate that the bar to refuse treatments based on these grounds is high and that in most cases risks are acceptable while success rates are sufficiently high to justify treatment.
Third, the risks of treatments should be balanced against the expected success rates of treatments. Risks of treatment are more acceptable if the success rates are higher. This obviously does not count for risks that only occur if the treatment is successful, for example pregnancy risks or risks for the offspring.
Finally, treatments without proven effectiveness should preferably be offered in the context of research. Uncertainty about their effectiveness should be shared with the individual(s) who undergo the treatment. While in a private context, where patients pay their own treatment, the issue of cost-effectiveness is less relevant, efficiency is important in a public system, where society pays for treatment. In the latter case, ineffective treatments (for example IVF for older women with success rates of 1 or 2%) can be delayed in favour of less expensive treatments, or even denied.
Koning A, Mol BW, Dondorp W. It is not justified to reject fertility treatment based on obesity. Hum Reprod Open. 2017 Jul 28;2017(2):hox009.
Braakhekke M, Kamphuis EI, Mol F, Norman RJ, Bhattacharya S, van der Veen F, Mol BW. Hum Reprod. Effectiveness and safety as outcome measures in reproductive medicine. 2015 Oct;30(10):2249-51.