bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic changes of ginsenosides in Panax quinquefolium fruit at different development stages measured using UHPLC‐Orbitrap MS
Authors: Jin Yinping , Hao Yan , Zhang Hao , Qu Zhengyi , Wang Yingping , Piao Xiangmin 
Published: February 2022

RationaleSome studies have shown that Panax quinquefolium fruit (PQF) could also be used as a potential medicinal resource. However, little is known about the composition of ginsenosides and their dynamic changes at different development stages of PQF. Therefore, this study is of great significance for the metabolomics and rational utilization of PQF.MethodsThe samples were analyzed using ultra‐high‐performance liquid chromatography combined with an Orbitrap mass spectrometer (UHPLC‐Orbitrap MS), and the method of metabonomics was applied to profile the dynamic changes of ginsenosides in PQF at different development stages.ResultsA total of 109 ginsenosides were identified or tentatively characterized. Samples collected from different development stages were significantly discriminated according to ginsenoside contents. A total of 25 potential chemical markers enabling the differentiation were discovered.ConclusionsFor the first time, the study developed an UHPLC‐Orbitrap MS‐based approach to detect ginsenoside in PQF at different development stages using a non‐targeted mode. This comprehensive phytochemical profile study revealed the structural diversity and discrimination of ginsenosides in PQF at different development stages, which could provide the basis for the metabolomics and rational application of PQF.
An advanced automation platform coupled with mass spectrometry for investigating in vitro human skin permeation of UV filters and excipients in sunscreen products
Authors: Zhang Jinhui , Yang Yang , Ashraf Muhammad , Cruz Celia N. , Lee Sau , Faustino Patrick J. 
Published: February 2022

RationaleSystemic absorption of UV‐filtering chemicals following topical application of sunscreens may present a safety concern. The Food and Drug Administration (FDA) had recommended an in vitro skin permeation test (IVPT) to evaluate the potential of this safety risk for the evaluation of sunscreens prior to clinical studies. Therefore, a sensitive and robust bioanalytical method(s) were required for IVPT studies of different topical sunscreen products.MethodsAn analytical procedure to quantitate sunscreen UV‐filtering components and excipients in IVPT samples including avobenzone, octocrylene, oxybenzone, ecamsule, methylparaben and propylparaben was developed employing a RapidFire 360 robotic sample delivery system coupled with a triple quadrupole mass spectrometer. The analytical procedure was developed and validated according to the requirements of the FDA Bioanalytical Method Validation Guidance for Industry (2018).ResultsThe analytical method provided a turnaround time of 12 seconds per sample and was determined to be accurate, precise, specific, and linear over the corresponding analytical ranges. The validated method was successfully applied for two IVPT studies for evaluating the skin permeation potential of UV‐filtering chemicals and assisting with the selection of the sunscreen products for the clinical study conducted by the FDA.ConclusionsThis work highlights the first analytical procedure that has applied a non‐chromatographic‐MS/MS automation platform to an in vitro biopharmaceutics study. The analytical platform simultaneously quantitated four UV filters and two excipients in complex media to evaluate their permeation in IVPT studies. The sample throughput and analytical performance of advanced automation platforms indicate their analytical procedure has the potential to significantly advance the efficiency of IVPT studies to evaluate permeation of a wide variety of UV chemical filters and excipients for topical OTC sunscreen products.
Assessing reproducibility of high‐throughput experiments in the case of missing data
Authors: Singh Roopali , Zhang Feipeng , Li Qunhua 
Published: February 2022

AbstractHigh‐throughput experiments are an essential part of modern biological and biomedical research. The outcomes of high‐throughput biological experiments often have a lot of missing observations due to signals below detection levels. For example, most single‐cell RNA‐seq (scRNA‐seq) protocols experience high levels of dropout due to the small amount of starting material, leading to a majority of reported expression levels being zero. Though missing data contain information about reproducibility, they are often excluded in the reproducibility assessment, potentially generating misleading assessments. In this article, we develop a regression model to assess how the reproducibility of high‐throughput experiments is affected by the choices of operational factors (eg, platform or sequencing depth) when a large number of measurements are missing. Using a latent variable approach, we extend correspondence curve regression, a recently proposed method for assessing the effects of operational factors to reproducibility, to incorporate missing values. Using simulations, we show that our method is more accurate in detecting differences in reproducibility than existing measures of reproducibility. We illustrate the usefulness of our method using a single‐cell RNA‐seq dataset collected on HCT116 cells. We compare the reproducibility of different library preparation platforms and study the effect of sequencing depth on reproducibility, thereby determining the cost‐effective sequencing depth that is required to achieve sufficient reproducibility.
Integrative taxonomy of the model liverwort Riella helicophylla (Riellaceae, Sphaerocarpales) reveals its extreme rarity and an overlooked widespread new species, R. macrocarpa
Authors: Segarra‐Moragues José Gabriel , Puche Felisa , Sabovljević Marko S. , Infante Marta , Heras Patxi 
Published: February 2022

AbstractRiella (Riellaceae) is a genus of rare, ephemeral, aquatic liverworts that includes some taxa specialized in growing submerged in brackish, seasonal water ponds and lagoons. One of these species, Riella helicophylla is the type of the genus. Apart from being of conservation concern, it has been used as a model organism for cytological and physiological processes. The species was described from Algeria in the mid‐nineteenth century and was not found elsewhere for almost a century, when it was discovered in central Spain. Nonetheless, those new populations were considered morphologically different and served to describe a new variety (var. macrocarpa), and a form (f. latealata) of the latter. The number of population records increased considerably in the following decades, especially in the late twentieth century; at the same time, it was discovered in several countries throughout the Mediterranean basin. Those reports, however, did not account for its infraspecific distinction. As part of a broader study of the genus, in this work, we have revisited the taxonomy of R. helicophylla based on an integrative approach considering morphological and molecular DNA sequence data. Our broadly sampled study revealed that R. helicophylla includes two morphotypes corresponding with the previously recognized varieties of this species. These varieties differ consistently in a number of morphological gametophytic and spore traits. Riella helicophylla was resolved as paraphyletic in phylogenies based on nuclear and plastid DNA sequences. The accessions clustered in two monophyletic clades in concert with morphology, supporting their recognition at the species level. Accordingly, a new combination is proposed, R. macrocarpa, which includes the neglected R. helicophylla var. macrocarpa and R. helicophylla var. macrocarpa f. latealata. Lectotypes are designated for the two latter taxa and for R. helicophylla. The two species are fully described and illustrated, and an updated identification key of the Mediterranean species is included. Updated information on the conservation status of both species is provided.
The momentum amplituhedron of SYM and ABJM from twistor-string maps
Authors: He Song , Kuo Chia-Kai , Zhang Yao-Qi 
Published: February 2022

Abstract
We study remarkable connections between twistor-string formulas for tree amplitudes in $$ \mathcal{N} $$
N
= 4 SYM and $$ \mathcal{N} $$
N
= 6 ABJM, and the corresponding momentum amplituhedron in the kinematic space of D = 4 and D = 3, respectively. Based on the Veronese map to positive Grassmannians, we define a twistor-string map from G+(2, n) to a (2n−4)-dimensional subspace of the 4d kinematic space where the momentum amplituhedron of SYM lives. We provide strong evidence that the twistor-string map is a diffeomorphism from G+(2, n) to the interior of momentum amplituhedron; the canonical form of the latter, which is known to give tree amplitudes of SYM, can be obtained as pushforward of that of former. We then move to three dimensions: based on Veronese map to orthogonal positive Grassmannian, we propose a similar twistor-string map from the moduli space $$ {\mathrm{\mathcal{M}}}_{0,n}^{+} $$

ℳ

0
,
n

+

to a (n−3)-dimensional subspace of 3d kinematic space. The image gives a new positive geometry which conjecturally serves as the momentum amplituhedron for ABJM; its canonical form gives the tree amplitude with reduced supersymmetries in the theory. We also show how boundaries of compactified $$ {\mathrm{\mathcal{M}}}_{0,n}^{+} $$

ℳ

0
,
n

+

map to boundaries of momentum amplituhedra for SYM and ABJM corresponding to factorization channels of amplitudes, and in particular for ABJM case the map beautifully excludes all unwanted channels.
Endpoint Sobolev bounds for fractional Hardy–Littlewood maximal operators
Authors: Weigt Julian 
Published: February 2022

AbstractLet $$0<\alpha <d$$

0
<
α
<
d

and $$1\le p<d/\alpha $$

1
≤
p
<
d
/
α

. We present a proof that for all $$f\in W^{1,p}({\mathbb {R}}^d)$$

f
∈

W

1
,
p

(

R

d

)

both the centered and the uncentered Hardy–Littlewood fractional maximal operator $${\mathrm {M}}_\alpha f$$

M
α

f

are weakly differentiable and $$ \Vert \nabla {\mathrm {M}}_\alpha f\Vert _{p^*} \le C_{d,\alpha ,p} \Vert \nabla f\Vert _p , $$

‖
∇

M
α

f
‖

p
∗

≤

C

d
,
α
,
p

‖
∇
f
‖

p

,

where $$ p^* = (p^{-1}-\alpha /d)^{-1} . $$

p
∗

=

(

p

-
1

-
α
/
d
)

-
1

.

In particular it covers the endpoint case $$p=1$$

p
=
1

for $$0<\alpha <1$$

0
<
α
<
1

where the bound was previously unknown. For $$p=1$$

p
=
1

we can replace $$W^{1,1}({\mathbb {R}}^d)$$

W

1
,
1

(

R

d

)

by $$\mathrm {BV}({\mathbb {R}}^d)$$

BV
(

R

d

)

. The ingredients used are a pointwise estimate for the gradient of the fractional maximal function, the layer cake formula, a Vitali type argument, a reduction from balls to dyadic cubes, the coarea formula, a relative isoperimetric inequality and an earlier established result for $$\alpha =0$$

α
=
0

in the dyadic setting. We use that for $$\alpha >0$$

α
>
0

the fractional maximal function does not use certain small balls. For $$\alpha =0$$

α
=
0

the proof collapses.
Physicochemical characterization of the recombinant lectin scytovirin and microbicidal activity of the SD1 domain produced in rice against HIV-1
Authors: Armario-Najera Victoria , Blanco-Perera Amaya , Shenoy Shilpa R. , Sun Yi , Marfil Silvia , Muñoz-Basagoiti Jordana , Perez-Zsolt Daniel , Blanco Julià , Izquierdo-Useros Nuria , Capell Teresa , O’Keefe Barry R. , Christou Paul 
Published: February 2022

Abstract
Key message
Rice-produced SD1 retains its physicochemical properties and provides efficient pre-exposure HIV-1 prophylaxis against infection in vitro.

Abstract
Scytovirin (SVN) is an HIV-neutralizing lectin that features two structural domains (SD1 and SD2) that bind to HIV-1 envelope glycoproteins. We expressed SD1 in rice seeds as a potential large-scale production platform and confirmed that rice-derived SD1 binds the HIV-1 envelope glycoprotein gp120 in vitro. We analyzed the thermodynamic properties of SD1 compared to full-size SVN (produced in E. coli) by isothermal titration and differential scanning calorimetry to characterize the specific interactions between SVN/SD1 and gp120 as well as to high-mannose oligosaccharides. SVN bound with moderate affinity (Kd = 1.5 µM) to recombinant gp120, with 2.5-fold weaker affinity to nonamannoside (Kd of 3.9 µM), and with tenfold weaker affinity to tetramannoside (13.8 µM). The melting temperature (Tm) of full-size SVN was 59.1 °C and the enthalpy of unfolding (ΔHunf) was 16.4 kcal/mol, but the Tm fell when SVN bound to nonamannoside (56.5 °C) and twice as much energy was required for unfolding (ΔHunf = 33.5 kcal/mol). Interestingly, binding to tetramannoside destabilized the structure of SD1 (ΔTm ~ 11.5 °C) and doubled the enthalpy of unfolding, suggesting a dimerization event. The similar melting phenomenon shared by SVN and SD1 in the presence of oligomannose confirmed their conserved oligosaccharide-binding mechanisms. SD1 expressed in transgenic rice was able to neutralize HIV-1 in vitro. SD1 expressed in rice, therefore, is suitable as a microbicide component.
DNA Methylation Alterations and Their Association with High Temperature Tolerance in Rice Anthesis
Authors: Li Bo , Cai Haiya , Liu Ke , An Bingzhuang , Wang Rong , Yang Fang , Zeng Changli , Jiao Chunhai , Xu Yanhao 
Published: February 2022

AbstractDNA methylation is an important epigenetic mechanism involved in gene regulation under environmental stresses in plants. However, little information is available regarding its responses to high temperature (HT) and association with HT tolerance in rice. In this study, fourteen rice genotypes were classified into the susceptible, moderate, and tolerant groups by the high temperature susceptibility index (HTSI) after HT treatment. The changes of DNA methylation in rice anthesis under normal and HT30 conditions were investigated using methylation-sensitive amplified polymorphism31 (MSAP). The MSAP results showed that the DNA methylation level significantly increased in the susceptible rice group and decreased in the tolerant rice group under HT treatment, while no significant difference was observed in the moderate rice group. More hypomethylation events were detected in the tolerant rice group, while more hypermethylation was detected in the susceptible rice group. Forty-four differentially methylated epiloci (DME) were generated under both control and HT conditions, which can clearly distinguish the susceptible, moderate, and tolerant genotypes via PCoA analysis. Approximately 43.18% of DMEs were determined to be tolerance-associated epiloci (TAEs). 63.15% TAEs were sequenced and annotated into 12 genes. Quantitative RT-PCR analysis showed that 12 TAE genes were mainly upregulated in 14 rice genotypes, and their expression levels were related to the HT tolerance of rice. Here, DEGs, generated from a number of genotypes, indicate higher probabilities for association with stress tolerance. Overall, these results suggest that DNA methylation regulation might play a key role in adaptation to HT stress in rice.
Inverse deformation analysis: an experimental and numerical assessment using the FEniCS Project
Authors: Mazier Arnaud , Bilger Alexandre , Forte Antonio E. , Peterlik Igor , Hale Jack S. , Bordas Stéphane P. A. 
Published: February 2022

AbstractIn this paper we develop a framework for solving inverse deformation problems using the FEniCS Project finite-element software. We validate our approach with experimental imaging data acquired from a soft silicone beam under gravity. In contrast with inverse iterative algorithms that require multiple solutions of a standard elasticity problem, the proposed method can compute the undeformed configuration by solving only one modified elasticity problem. This modified problem has a complexity comparable to the standard one. The framework is implemented within an open-source pipeline enabling the direct and inverse deformation simulation directly from imaging data. We use the high-level unified form language (UFL) of the FEniCS Project to express the finite-element model in variational form and to automatically derive the consistent Jacobian. Consequently, the design of the pipeline is flexible: for example, it allows the modification of the constitutive models by changing a single line of code. We include a complete working example showing the inverse deformation of a beam deformed by gravity as supplementary material.
Digital templating cementless short stem total hip arthroplasty: is there a difference in planning adherence between the direct anterior approach and minimally invasive anterolateral approach?
Authors: Luger Matthias , Feldler Sandra , Schauer Bernhard , Hochgatterer Rainer , Gotterbarm Tobias , Klasan Antonio 
Published: February 2022

Abstract
Purpose
Minimally invasive approaches (MIS) in total hip arthroplasty (THA) show inconsistent findings regarding planning adherence in digital templating. The purpose of this study is to evaluate any difference in planning adherence between the direct anterior approach (DAA) and an anterolateral MIS approach (AL MIS) in cementless short stem THA.

Methods
A single surgeon series of 222 THAs in 208 patients with an uncemented short curved stem and a bi-hemispherical acetabular cup were screened for inclusion. A total of 118 THAs were implanted via the DAA and 72 THAs via the AL MIS were included. The planning adherence for the offset option, stem size and the acetabular cup were retrospectively evaluated.

Results
Planning adherence for cup size (perfect match: p = 0.763; ± 1 size: p = 0.124), offset option (0.125) and stem size (perfect match: p = 0.275; ± 1 size: p = 0.552) did not show any statistical significance. Preoperative diagnosis of avascular necrosis of the femoral head in AL MIS approach (OR 6.045; CI 1.153–31.696) or mild hip dysplasia in the general cohort poses (OR 11.789; CI 1.386–100.293) a significant risk for inadequate prediction of the offset option. Conclusion: digital templating for THA with an uncemented short curved stem and a bi-hemispherical acetabular cup show comparable results between a direct anterior approach and a minimally invasive anterolateral approach in supine position. Surgeons should be aware of a low planning adherence for this type of short stem in minimally invasive approaches.

Conclusion
Digital templating for THA with an uncemented short curved stem and a bi-hemispherical acetabular cup show comparable results between a direct anterior approach and a minimally invasive anterolateral approach in supine position. Surgeons should be aware of a low planning adherence for this type of short stem in minimally invasive approaches.
Length is not all that matters: testing the role of number identity and the ratio of fillers in comparisons of multi-digits with different digit length
Authors: García-Orza Javier , Gutiérrez-Cordero Ismael , Larios Carlos , Csilinkó Anikó , Álvarez-Montesinos Juan Antonio 
Published: February 2022

AbstractResearch in multi-digit number comparison usually considers stimuli with the same number of digits (e.g., 3452 vs. 7831). Surprisingly, there is almost no research on the comparison of numbers that differ in length (e.g., 995 vs. 1000), which demands a focus on the number of digits in each multi-digit, despite the fact that the role of number length has been explicitly acknowledged in componential models of multi-digit processing. Our study explores whether the comparison of pairs of natural numbers that differ in length is affected by the identity of the leftmost digit of each multi-digit, and asks what is the effect of having variable proportions of trials with pairs of numbers of the same-length in the task. Across three studies participants compared numbers in blocks with different proportions of same-length multi-digit pairs (Experiment 1 and 2: 25% vs. 50% vs. 75%; Experiment 3: 0% vs. 50%). Stimuli in the different-length condition were length-digit congruent (the number with more digits starting with a larger digit: 2384 vs. 107) or length-digit incongruent (the number with more digits starting with a smaller number: 2675 vs. 398). Response times were shorter in length-digit congruent pairs than in the incongruent pairs. Unexpectedly, this effect was only slightly modulated by the proportion of same-/different-length multi-digit pairs in the experimental set. Despite its perceptual saliency, length is not the only information considered when comparing different-length numbers. The leftmost-digit is also taken into account, with variable relevance here, depending on the characteristics of the stimuli set.
Finite free convolutions of polynomials
Authors: Marcus Adam W. , Spielman Daniel A. , Srivastava Nikhil 
Published: February 2022

AbstractWe study three convolutions of polynomials in the context of free probability theory. We prove that these convolutions can be written as the expected characteristic polynomials of sums and products of unitarily invariant random matrices. The symmetric additive and multiplicative convolutions were introduced by Walsh and Szegö in different contexts, and have been studied for a century. The asymmetric additive convolution, and the connection of all of them with random matrices, is new. By developing the analogy with free probability, we prove that these convolutions produce real rooted polynomials and provide strong bounds on the locations of the roots of these polynomials.
Hemorrhagic cystitis in allogeneic stem cell transplantation: a role for age and prostatic hyperplasia
Authors: Galli Eugenio , Sorà Federica , Di Gianfrancesco Luca , Giammarco Sabrina , Metafuni Elisabetta , Limongiello Maria Assunta , Innocenti Idanna , Autore Francesco , Laurenti Luca , Chiusolo Patrizia , Bacigalupo Andrea , Sica Simona 
Published: February 2022

Abstract
Purpose
Hemorrhagic cystitis (HC) is a frequent complication of allogeneic hematopoietic stem-cell transplantation (HSCT). HC worsens transplant outcomes and patient wellbeing in terms of pain, hospitalization, and need for supportive care. A deeper understanding of the risk factors of HC may lead to more intensive prevention in high-risk patients.

Methods
In this report, we analyzed 237 consecutive patients who received HSCT with the aim of identifying possible risk factors for HC and their consequences, with a particular focus on transplant- and gender-related risk factors.

Results
HC occurred in 17% of patients, with a higher incidence in males (21% vs 11%, p = 0.03). Risk factors identified for HC included age over 55 years, male recipient, HLA mismatch, reduced intensity conditioning, and cyclophosphamide-based graft-versus-host disease (GVHD) prophylaxis. Increased HC was seen in patients with grade II–IV acute GVHD and detectable BKV and JCV viruria. In a multivariate model, increased age remained significant (p = 0.013). Patients with HC had longer hospitalizations and increased non-relapse mortality (NRM). Among male recipients, independent risk factors for HC included age (p = 0.016) and prostate volume (p = 0.016). Prostatic hyperplasia (volume more than 40 cm3) occurred in 33% of male patients, of which 32% developed HC (compared with 16% of patients without prostatic hyperplasia; p = 0.032).

Conclusions
Age is the most important risk factor for HC. Additional potential risk factors include cyclophosphamide-based GVHD prophylaxis and HLA mismatch. Among male recipients, prostatic hyperplasia is an additional independent risk factor. As HC is common and associated with prolonged hospitalization, more intensive prophylactic strategies should be considered in high-risk patients.