bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fixing stray traditions in gingers: The identity and nomenclatural history of Zingiber neesanum and other entwined names
Authors: Patil Sameer , Shinde Rajendra D. , Leong‐Škorničková Jana , Chaudhari Rushabh 
Published: September 2021

AbstractThe identities of two historical names, Zingiber neesanum (≡ Alpinia neesana) and Z. macrostachyum are re‐investigated. Both have been considered to represent the same taxonomic entity by various workers in the past 160 years. Yet, based on traditional usage, they were applied to two distinct taxa occurring in the Western Ghats (India), both superficially similar by having long‐stalked inflorescences, but much distinct in flower colour and overall morphology. Alpinia neesana was originally described only from fruiting material, while Z. macrostachyum was described from flowering material of a species with white flowers. Dalzell's presumption that his taxon was identical to Graham's, and unambiguous inclusion of A. neesana in his description made his name nomenclaturally superfluous and illegitimate. After realising the illegitimacy of Dalzell's name, a new combination was created in Zingiber for A. neesana. The name Z. neesanum continued to be applied sensu Dalzell to the white‐flowered species mainly in the central and southern Western Ghats, but it was also applied to a yellow‐flowered species in the northern Western Ghats, for which another name, Z. diwakarianum, was proposed recently. Despite the absence of any original material relating to Graham's or Dalzell's descriptions, re‐collections from the type localities prove beyond any reasonable doubt that the yellow‐flowered species is the true Z. neesanum, making Z. diwakarianum a synonym, and that the existing name Z. anamalayanum has to be applied to the white‐flowered species, originally described by Dalzell as Z. macrostachyum. The significance of authentic primary data sources concerning botanical history such as correspondence and manuscripts of collectors and botanists, and the importance of making these resources widely accessible through digitisation are highlighted.
Botanical history and typification in the Tillandsia ionantha complex
Authors: Ancona Juan José , Pinzón Juan Pablo , Ortiz Díaz Juan Javier , Morillo Ivón Ramírez , Tun‐Garrido Juan , Palma‐Silva Clarisse , Till Walter 
Published: September 2021

AbstractA historical compilation of the routes and botanists of the 19th century was made about the holotype of Tillandsia ionantha. This species was described by J.E. Planchon in 1855 from an illustration of a plant grown in L. Van Houtte's greenhouses. After a thorough revision of the main works we concluded that the specimen that served as a model for the T. ionantha illustration is of Mexican origin and was collected by the A. Ghiesbreght team between 1836 and 1845 in the Huatusco region, Veracruz, in northeastern Mexico. Moreover, T. rubentifolia is here lectotypified, and T. scopus is considered a name not validly published.
Chemical imaging and machine learning for sub‐classification of oesophageal tissue histology
Authors: Keogan Abigail , Nguyen Thi Nguyet Que , Phelan James J. , O'Farrell Naoimh , Lynam‐Lennon Niamh , Doyle Brendan , O'Toole Dermot , Reynolds John V. , O'Sullivan Jacintha , Meade Aidan D. 
Published: September 2021

AbstractFourier Transform Infrared (FTIR) based chemical imaging is a powerful, non‐destructive and label‐free biophotonic technique, which spatially acquires bio‐molecularly relevant information in histopathology. Cancer detection with objective chemical imaging techniques is relatively well established, though detection of pre‐cancer stages within a continuum from normal tissue to cancer remains challenging. Here machine learning with chemical imaging was used to provide an objective classification pipeline for oesophageal tissues pathologically classified as normal, oesophagitis, dysplasia, Barrett's disease and cancer. Spectral images were segmented using a k‐means cluster validity indices approach and clustered spectra were classified using partial least squares discriminant analysis. Classification performances approached a receiver operator characteristic area‐under‐the‐curve (ROC‐AUC) of 0.90 for binary classification tasks (eg, normal vs Barrett's). Isolated histopathological substructures were identified which delivered a ROC‐AUC in of ~0.69 in classifying into each of the five‐classes. This work may provide the means to assist pathologist diagnoses of intermediate pre‐cancer stages.
Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean
Authors: Cruz Maribel , Arbelaez Juan David , Loaiza Katherine , Cuasquer Juan , Rosas Juan , Graterol Eduardo 
Published: September 2021

AbstractRice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release. In this study, a genome‐wide association study (GWAS), marker‐assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from −0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain‐quality traits. These markers individually explained 51–75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS. Cross‐validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.
Genome‐enabled prediction for sparse testing in multi‐environmental wheat trials
Authors: Crespo‐Herrera Leonardo , Howard Reka , Piepho Hans‐Peter , Pérez‐Rodríguez Paulino , Montesinos‐Lopez Osval , Burgueño Juan , Singh Ravi , Mondal Suchismita , Jarquín Diego , Crossa Jose 
Published: September 2021

AbstractSparse testing in genome‐enabled prediction in plant breeding can be emulated throughout different line allocations where some lines are observed in all environments (overlap) and others are observed in only one environment (nonoverlap). We studied three general cases of the composition of the sparse testing allocation design for genome‐enabled prediction of wheat (Triticum aestivum L.) breeding: (a) completely nonoverlapping wheat lines in environments, (b) completely overlapping wheat lines in all environments, and (c) a proportion of nonoverlapping/overlapping wheat lines allocated in the environments. We also studied several cases in which the size of the testing population was systematically decreased. The study used three extensive wheat data sets (W1, W2, and W3). Three different genome‐enabled prediction models (M1–M3) were used to study the effect of the sparse testing in terms of the genomic prediction accuracy. Model M1 included only main effects of environments and lines; M2 included main effects of environments, lines, and genomic effects; whereas the remaining model (M3) also incorporated the genomic × environment interaction (GE). The results show that the GE component of the genome‐based model M3 captures a larger genetic variability than the main genomic effects term from models M1 and M2. In addition, model M3 provides higher prediction accuracy than models M1 and M2 for the same allocation designs (different combinations of nonoverlapping/overlapping lines in environments and training set sizes). Overlapped sets of 30–50 lines in all the environments provided stable genomic‐enabled prediction accuracy. Reducing the size of the testing populations under all allocation designs decreases the prediction accuracy, which recovers when more lines are tested in all environments. Model M3 offers the possibility of maintaining the prediction accuracy throughout both extreme situations of all nonoverlapping lines and all overlapping lines.
Laparoscopic treatment for a prostatic cyst in a dog
Authors: Comas Collgrós Núria , Carbonell Rosselló Gabriel , Jiménez Peláez Manuel 
Published: September 2021

AbstractTreatment of choice for prostatic cysts is partial or complete resection, drainage and omentalisation, commonly performed through a caudal laparotomy. The aim of this case report is to describe for the first time the laparoscopic treatment of a prostatic cyst in a dog. Laparoscopy was elected to avoid the morbidity and disadvantages related to a parapreputial laparotomy approach. Partial resection, drainage and omentalisation of a prostatic cyst was performed through four abdominal 5 mm ports situated on midline caudal umbilical, mid left abdominal region and two on the right caudal abdomen. The patient recovered quickly, uneventfully and without recurrence during the 15‐month follow‐up period.
Metro Manila's 2019 water crisis: Of efficiency traps and dry taps
Authors: Torio Philamer C. , Mendoza Ronald U. , Torres Ayn G. 
Published: September 2021

AbstractIn 2019, Metro Manila experienced a water supply crisis, barely 2 years after the government and its private concessionaires were given international recognition for a successful water privatization, with success defined in terms of high operating efficiencies and improved service levels. These service‐level improvements, however, brought about a surge in consumer demand, which necessitated the construction of a new water supply infrastructure. Regulatory failures resulting in nondelivery of the infrastructure effectively negated and trapped the efficiency gains that were built slowly over the years, at a cost of US$5.4 billion. Such failures resulted in public indignation over dry household taps, as well as a presidential anger that threatened to cancel the program in its entirety. Using the lessons learned from this crisis, the paper enumerates measures to help unlock the traps set by these regulatory failures.
Population Design for Synthetic Gene Circuits
Authors: Turpin Baptiste , Bijman Eline Y. , Kaltenbach Hans-Michael , Stelling Jörg 
Published: September 2021

AbstractSynthetic biologists use and combine diverse biological parts to build systems such as genetic circuits that perform desirable functions in, for example, biomedical or industrial applications. Computer-aided design methods have been developed to help choose appropriate network structures and biological parts for a given design objective. However, they almost always model the behavior of the network in an average cell, despite pervasive cell-to-cell variability. Here, we present a computational framework to guide the design of synthetic biological circuits while accounting for cell-to-cell variability explicitly. Our design method integrates a NonLinear Mixed-Effect (NLME) framework into an existing algorithm for design based on ordinary differential equation (ODE) models. The analysis of a recently developed transcriptional controller demonstrates first insights into design guidelines when trying to achieve reliable performance under cell-to-cell variability. We anticipate that our method not only facilitates the rational design of synthetic networks under cell-to-cell variability, but also enables novel applications by supporting design objectives that specify the desired behavior of cell populations.
BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems
Authors: Saxena Gaurav , Ponce-de-Leon Miguel , Montagud Arnau , Vicente Dorca David , Valencia Alfonso 
Published: September 2021

AbstractMulti-scale simulations require parallelization to address large-scale problems, such as real-sized tumor simulations. BioFVM is a software package that solves diffusive transport Partial Differential Equations for 3-D biological simulations successfully applied to tissue and cancer biology problems. Currently, BioFVM is only shared-memory parallelized using OpenMP, greatly limiting the execution of large-scale jobs in HPC clusters. We present BioFVM-X: an enhanced version of BioFVM capable of running on multiple nodes. BioFVM-X uses MPI+OpenMP to parallelize the generic core kernels of BioFVM and shows promising scalability in large 3-D problems with several hundreds diffusible substrates and $$\approx $$
≈
0.5 billion voxels. The BioFVM-X source code, examples and documentation, are available under the BSD 3-Clause license at https://gitlab.bsc.es/gsaxena/biofvm_x.
T
$$ \overline{T} $$-flow effects on torus partition functions
Authors: He Song , Sun Yuan , Zhang Yu-Xuan 
Published: September 2021

Abstract
In this paper, we investigate the partition functions of conformal field theories (CFTs) with the T$$ \overline{T} $$

T
¯

deformation on a torus in terms of the perturbative QFT approach. In Lagrangian path integral formalism, the first- and second-order deformations to the partition functions of 2D free bosons, free Dirac fermions, and free Majorana fermions on a torus are obtained. The corresponding Lagrangian counterterms in these theories are also discussed. The first two orders of the deformed partition functions and the first-order vacuum expectation value (VEV) of the first quantum KdV charge obtained by the perturbative QFT approach are consistent with results obtained by the Hamiltonian formalism in literature.
Spontaneously broken boosts in CFTs
Authors: Komargodski Zohar , Mezei Márk , Pal Sridip , Raviv-Moshe Avia 
Published: September 2021

Abstract
Conformal Field Theories (CFTs) have rich dynamics in heavy states. We describe the constraints due to spontaneously broken boost and dilatation symmetries in such states. The spontaneously broken boost symmetries require the existence of new low-lying primaries whose scaling dimension gap, we argue, scales as O(1). We demonstrate these ideas in various states, including fluid, superfluid, mean field theory, and Fermi surface states. We end with some remarks about the large charge limit in 2d and discuss a theory of a single compact boson with an arbitrary conformal anomaly.
Revisiting Coleman-de Luccia transitions in the AdS regime using holography
Authors: Ghosh Jewel K. , Kiritsis Elias , Nitti Francesco , Witkowski Lukas T. 
Published: September 2021

Abstract
Coleman-de Luccia processes for AdS to AdS decays in Einstein-scalar theories are studied. Such tunnelling processes are interpreted as vev-driven holographic RG flows of a quantum field theory on de Sitter space-time. These flows do not exist for generic scalar potentials, which is the holographic formulation of the fact that gravity can act to stabilise false AdS vacua. The existence of Coleman-de Luccia tunnelling solutions in a potential with a false AdS vacuum is found to be tied to the existence of exotic RG flows in the same potential. Such flows are solutions where the flow skips possible fixed points or reverses direction in the coupling. This connection is employed to construct explicit potentials that admit Coleman-de Luccia instantons in AdS and to study the associated tunnelling solutions. Thin-walled instantons are observed to correspond to dual field theories with a parametrically large value of the dimension ∆ for the operator dual to the scalar field, casting doubt on the attainability of this regime in holography. From the boundary perspective, maximally symmetric instantons describe the probability of symmetry breaking of the dual QFT in de Sitter. It is argued that, even when such instantons exist, they do not imply an instability of the same theory on flat space or on R × S3.
Derivative corrections to the Heisenberg-Euler effective action
Authors: Karbstein Felix 
Published: September 2021

Abstract
We show that the leading derivative corrections to the Heisenberg-Euler effective action can be determined efficiently from the vacuum polarization tensor evaluated in a homogeneous constant background field. After deriving the explicit parameter-integral representation for the leading derivative corrections in generic electromagnetic fields at one loop, we specialize to the cases of magnetic- and electric-like field configurations characterized by the vanishing of one of the secular invariants of the electromagnetic field. In these cases, closed-form results and the associated all-orders weak- and strong-field expansions can be worked out. One immediate application is the leading derivative correction to the renowned Schwinger-formula describing the decay of the quantum vacuum via electron-positron pair production in slowly-varying electric fields.
Extract the energy scale of anomalous γγ → W+W− scattering in the vector boson scattering process using artificial neural networks
Authors: Yang Ji-Chong , Chen Jin-Hua , Guo Yu-Chen 
Published: September 2021

Abstract
As a model independent approach to search for the signals of new physics (NP) beyond the Standard Model (SM), the SM effective field theory (SMEFT) draws a lot of attention recently. The energy scale of a process is an important parameter in the study of an EFT such as the SMEFT. However, for the processes at a hadron collider with neutrinos in the final states, the energy scales are difficult to reconstruct. In this paper, we study the energy scale of anomalous γγ → W+W− scattering in the vector boson scattering (VBS) process pp → jjℓ+ℓ−ν$$ \overline{\nu} $$

ν
¯

at the large hadron collider (LHC) using artificial neural networks (ANNs). We find that the ANN is a powerful tool to reconstruct the energy scale of γγ → W+W− scattering. The factors affecting the effects of ANNs are also studied. In addition, we make an attempt to interpret the ANN and arrive at an approximate formula which has only five fitting parameters and works much better than the approximation derived from kinematic analysis. With the help of ANN approach, the unitarity bound is applied as a cut on the energy scale of γγ → W+W− scattering, which is found to has a significant suppressive effect on signal events. The sensitivity of the process pp → jjℓ+ℓ−ν$$ \overline{\nu} $$

ν
¯

to anomalous γγWW couplings and the expected constraints on the coefficients at current and possible future LHC are also studied.
Time-dependent study of KS → π+π− decays for flavour physics measurements
Authors: Pakhlov P. , Popov V. 
Published: September 2021

Abstract
Nowadays High Energy Physics experiments can accumulate unprecedented statistics of heavy flavour decays that allows to apply new methods, based on the study of very rare phenomena, which used to be just desperate. In this paper we propose a new method to measure composition of K0-$$ \overline{K} $$

K
¯

0, produced in a decay of heavy hadrons. This composition contains important information, in particular about weak and strong phases between amplitudes of the produced K0 and $$ \overline{K} $$

K
¯

0. We consider possibility to measure these parameters with time-dependent K0 → π+π− analysis. Due to C P -violation in kaon mixing time-dependent decay rates of K0 and $$ \overline{K} $$

K
¯

0 differ, and the initial amplitudes revealed in the CP-violating decay pattern. We perform phenomenological study of K0 decay evolution initially produced as a combination $$ a\left.|{K}^0(t)\right\rangle +b\left.|{\overline{K}}^0(t)\right\rangle $$
a

K
0

t

+
b

K
¯

0

t

, where a and b, complex amplitudes, could also be dependent on decay time of heavy mother particle. In particular we consider cases of charmed hadrons decays: D+ → K0π+, $$ {D}_s^{+} $$

D
s
+

→ K0K+, Λ → pK0 and with some assumptions D0 → K0π0. This can be used to test the sum rule for charmed mesons and to obtain input for the full constraint of the two body amplitudes of D-mesons.
Health-related quality of life and return to work 1 year after major trauma from a network perspective
Authors: van Ditshuizen Jan C. , van Lieshout Esther M. M. , van Beeck Ed F. , Verhofstad Michiel H. J. , den Hartog Dennis ,   Dutch Trauma Registry Southwest, Soesman N. M. R. , Jakma T. S. C. , Waleboer M. , Staarink M. , Bruijninckx M. M. M. , Cardon A. Y. M. V. P. , den Hoed P. T. , Roukema G. R. , van der Vlies C. H. , Schep N. W. L. , van de Schoot L. 
Published: September 2021

Abstract
Introduction
Major trauma often results in long-term disabilities. The aim of this study was to assess health-related quality of life, cognition, and return to work 1 year after major trauma from a trauma network perspective.

Methods
All major trauma patients in 2016 (Injury Severity Score > 15, n = 536) were selected from trauma region Southwest Netherlands. Eligible patients (n = 365) were sent questionnaires with the EQ-5D-5L and questions on cognition, level of education, comorbidities, and resumption of paid work 1 year after trauma.

Results
A 50% (n = 182) response rate was obtained. EQ-US and EQ-VAS scored a median (IQR) of 0.81 (0.62–0.89) and 70 (60–80), respectively. Limitations were prevalent in all health dimensions of the EQ-5D-5L; 90 (50%) responders reported problems with mobility, 36 (20%) responders reported problems with self-care, 108 (61%) responders reported problems during daily activities, 129 (73%) responders reported pain or discomfort, 70 (39%) responders reported problems with anxiety or depression, and 102 (61%) of the patients reported problems with cognition. Return to work rate was 68% (37% full, 31% partial). A median (IQR) EQ-US of 0.89 (0.82–1.00) and EQ-VAS of 80 (70–90) were scored for fully working responders; 0.77 (0.66–0.85, p < 0.001) and 70 (62–80, p = 0.001) for partial working respondents; and 0.49 (0.23–0.69, p < 0.001) and 55 (40–72, p < 0.001) for unemployed respondents.

Conclusion
The majority experience problems in all health domains of the EQ-5D-5L and cognition. Return to work status was associated with all health domains of the EQ-5D-5L and cognition.