bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convex Hulls of Random Order Types
Authors: Goaoc Xavier , Welzl Emo 
Published: December 2022

We establish the following two main results on order types of points in general position in the plane (realizable simple planar order types, realizable uniform acyclic oriented matroids of rank 3):

(a)

The number of extreme points in an
n
-point order type, chosen uniformly at random from all such order types, is on average 4+
o
(1). For labeled order types, this number has average

\(4- \mbox{$\frac{8}{n^2 - n +2}$}\)

and variance at most 3.

(b)

The (labeled) order types read off a set of
n
points sampled independently from the uniform measure on a convex planar domain, smooth or polygonal, or from a Gaussian distribution are concentrated, i.e., such sampling typically encounters only a vanishingly small fraction of all order types of the given size.

Result (a) generalizes to arbitrary dimension
d
for labeled order types with the average number of extreme points 2
d
+
o
(1) and constant variance. We also discuss to what extent our methods generalize to the abstract setting of uniform acyclic oriented matroids. Moreover, our methods show the following relative of the Erdős-Szekeres theorem: for any fixed
k
, as
n
→ ∞, a proportion 1 -
O
(1/
n
) of the
n
-point simple order types contain a triangle enclosing a convex
k
-chain over an edge.

For the unlabeled case in (a), we prove that for any antipodal, finite subset of the two-dimensional sphere, the group of orientation preserving bijections is cyclic, dihedral, or one of
A
4
,
S
4
, or
A
5
(and each case is possible). These are the finite subgroups of
SO
(3) and our proof follows the lines of their characterization by Felix Klein.
Acute and Subchronic Toxicity Studies on the Aqueous Extract of the Plant Mixture (Bidens pilosa and Cymbopogon citratus Aerial Parts) in Rat Model
Authors: Tcheutchoua Yannick Carlos , Bilanda Danielle Claude , Mengue Ngadena Yolande Sandrine , Djomeni Dzeufiet Paul Désiré , Owona Pascal Emmanuel , Goufani Ronald Bidingha á , Fifen Rodrigue Ngapout , Nguegan Lohik Mbolang , Noubom Michel , Dimo Théophile , Kamtchouing Pierre 
Published: December 2022

Bidens pilosa (B. pilosa) and Cymbopogon citratus (C. citratus) are plants used individually or in combination in the traditional treatment of several ailments such as cardiovascular disorders. In order to valorise their traditional use, a toxicological study was conducted on the aqueous extract of the mixture of aerial parts of B. pilosa and C. citratus. The acute and subchronic toxicity studies were conducted according to the OECD 425 and 407 guidelines. Regarding the acute study, the aqueous extract of the mixture of B. pilosa and C. citratus 50 : 50 (2000 and 5000 mg/kg) was administered once to rats of both sexes. In the subchronic study, the aqueous extract of the mixture of B. pilosa and C. citratus (200, 400 and 800 mg/kg) was administered once daily to rats for 28 days. The aqueous extract of the mixture of B. pilosa and C. citratus (2000 and 5000 mg/kg) did not cause death and did not induce any apparent sign of toxicity during the 14 days of observation. The DL50 of the extract is therefore greater than 5000 mg/kg. Taken daily for 28 days, the extract had no significant effect on selected parameters (creatinine, AST, ALT, urea, and uric acid) of renal and hepatic function, as well as on the number of some blood cells. However, the aqueous extract of the mixture of B. pilosa and C. citratus (200 and 400 mg/kg) caused a significant (

p

<

0.05

;

p

<

0.001
,

respectively) decrease in creatinine levels in male rats as compared to normal control animals. In females, the aqueous extract of the mixture of B. pilosa and C. citratus (200 and 400 mg/kg) resulted in a significant (

p

<

0.05

) increase in total cholesterol levels as compared to normal control animals. The study showed that the aqueous extract of the mixture of B. pilosa and C. citratus has a low toxicity and does not cause any injury to the liver, kidney, lungs, or spleen.
The limits of mtDNA analysis for determining the provenance of invasive species: a midwife toad example
Authors: Vliegenthart Chris , van de Vrede Maurits , den Boer Ingrid , Gilbert Maarten J. , Lemmers Pim , France James , de Visser Manon C. , Struijk Richard P.J.H. , Wielstra Ben 
Published: December 2022

Abstract
For most if not all European herpetofauna, range-wide mtDNA phylogeographies have been published. This facilitates establishing the provenance of introduced populations. However, precision is contingent on the spatial genetic structure across the range of the taxon under study and, in particular, from where within that range the introduction was sourced. In the Netherlands, the common midwife toad, Alytes obstetricans, only naturally occurs in the extreme southeast and is on the decline there. Yet, introduced populations thrive elsewhere in the country. We use mtDNA analysis to try to determine the origin of two introduced populations along the Dutch coast, in the city of The Hague and the dune area Meijendel. We compiled a database of hundreds of individuals from throughout the distribution range and added over 130 individuals from both native and introduced populations from the Netherlands, Belgium and Germany. The mtDNA haplotypes found in the introduced populations are associated with postglacial expansion. The main haplotype predominates in the natural range in the Netherlands, but also occurs much more widely across western Europe, north of the Pyrenees. A closely related haplotype, newly identified from The Hague, was not found in the native Netherlands range, suggesting an origin from abroad. The combination of low phylogeographic resolution and low sampling density in the postglacially colonized part of the range hampers our ability to determine the provenance of the introduced A. obstetricans populations.
Many Amersfoort hands: Revisiting the making of Albert Eckhout’s Brazilian paintings (1641-1643)
Authors: Wadum Jørgen 
Published: December 2022

Albert Eckhout’s twenty-one paintings, signed and dated 1641-1643, kept at the National Museum of Denmark, has stirred much speculation as to their making, meaning, and function. Eight impressive larger-than-life depictions of native Brazilian inhabitants and a huge dancing scene of the Tarairiu Indians were presented as gifts to the Danish King Frederik III (1609-1670) in 1654, together with twelve almost square still lifes of exotic fruits and vegetables from Brazil. The present was from the initiator of the paintings, Johan Maurits van Nassau-Siegen (1604-1679), the governor of the Dutch possessions in north-eastern Brazil.
Following on the archival, historical and technical reports that have been presented over the years, a re-evaluation of the technical examinations combined with new comparative research points to a more complex genesis of the paintings. The canvases and ground layers suggest that the tall single-figure pieces were made in one batch, while the large dancing scene and the still-lifes were prepared in a small number of separate batches. Infrared imaging visualises different approaches in paint handling within the group of nine figure pieces. The working up of the final paint layer in the faces of the figures has been approached in two different ways, either opaquely or with semi-transparent layers in the shadow areas. Idiosyncratic manners of rendering the eyes complement these findings and reveal details hardly studied so far.
The article concludes that the Tupi man, the Black man, and the Mulatto man are painted in a different and more transparent technique. Further, the manner of mixing black paint with white to render a nuanced whiteness of the eyes of the three figures, is not found in any of the other six paintings. These tall figures were painted by another hand than Eckhout, and most probably someone active in Jacob van Campen’s large Randenbroek workshop in Amersfoort. Here, together with the still anonymous painter, Eckhout completed the impressive series of large Brazilian figures and twelve still lifes around 1647-1650. This research exemplifies the seventeenth-century collaborative practice of working on larger commissions, yet all the works continue to demonstrate Eckhout’s legacy and how studies from his Brazilian sojourn were used by a larger community of artists in the Netherlands to satisfy the need for exotic images of the time.
A New Paradigm for Medium-Range Severe Weather Forecasts: Probabilistic Random Forest–Based Predictions
Authors: Hill Aaron J. , Schumacher Russ S. , Jirak Israel L. 
Published: December 2022

Abstract
Historical observations of severe weather and simulated severe weather environments (i.e., features) from the Global Ensemble Forecast System v12 (GEFSv12) Reforecast Dataset (GEFS/R) are used in conjunction to train and test random forest (RF) machine learning (ML) models to probabilistically forecast severe weather out to days 4–8. RFs are trained with ∼9 years of the GEFS/R and severe weather reports to establish statistical relationships. Feature engineering is briefly explored to examine alternative methods for gathering features around observed events, including simplifying features using spatial averaging and increasing the GEFS/R ensemble size with time lagging. Validated RF models are tested with ∼1.5 years of real-time forecast output from the operational GEFSv12 ensemble and are evaluated alongside expert human-generated outlooks from the Storm Prediction Center (SPC). Both RF-based forecasts and SPC outlooks are skillful with respect to climatology at days 4 and 5 with diminishing skill thereafter. The RF-based forecasts exhibit tendencies to slightly underforecast severe weather events, but they tend to be well-calibrated at lower probability thresholds. Spatially averaging predictors during RF training allows for prior-day thermodynamic and kinematic environments to generate skillful forecasts, while time lagging acts to expand the forecast areas, increasing resolution but decreasing overall skill. The results highlight the utility of ML-generated products to aid SPC forecast operations into the medium range.

Significance Statement
Medium-range severe weather forecasts generated from statistical models are explored here alongside operational forecasts from the Storm Prediction Center (SPC). Human forecasters at the SPC rely on traditional numerical weather prediction model output to make medium-range outlooks and statistical products that mimic operational forecasts can be used as guidance tools for forecasters. The statistical models relate simulated severe weather environments from a global weather model to historical records of severe weather and perform noticeably better than human-generated outlooks at shorter lead times (e.g., day 4 and 5) and are capable of capturing the general location of severe weather events 8 days in advance. The results highlight the value in these data-driven methods in supporting operational forecasting.
Therapy selection for Hodgkin lymphoma in sickle cell disease: balancing risks and benefits
Authors: Fraley Claire E. , McKinney Christopher , Nuss Rachelle , Franklin Anna R. K. 
Published: December 2022

Abstract
Advances in treatment have reduced mortality from Hodgkin lymphoma; therefore, greater attention should be focused on minimizing the late effects. A variety of risk-adapted treatment regimens exist that prioritize disease presentation but not patient-specific comorbidities. Herein, we describe a patient with sickle cell disease diagnosed with Hodgkin lymphoma and the considerations made in treatment planning to minimize therapy-related acute toxicity and late effects that overlap with the patient’s preexisting sickle cell disease complications.
Generation of a humanized afucosylated BAFF-R antibody with broad activity against human B-cell malignancies
Authors: Dong Zhenyuan , Song Joo Y. , Thieme Elana , Anderson Aaron , Oh Elizabeth , Cheng Wesley A. , Kuang Benjamin Z. , Lee Vincent , Zhang Tiantian , Wang Zhe , Szymura Szymon , Smith D. Lynne , Zhang Jianbing , Nian Weihong , Zheng Xintong , He Feng , Zhou Qing , Cha Soung-chul , Danilov Alexey V. , Qin Hong , Kwak Larry W. 
Published: December 2022

Abstract
B-cell activating factor receptor (BAFF-R) is a mature B-cell survival receptor, which is highly expressed in a wide variety of B-cell malignancies but with minimal expression in immature B cells. These properties make BAFF-R an attractive target for therapy of B-cell lymphomas. We generated a novel humanized anti BAFF-R monoclonal antibody (mAb) with high specificity and potent in vitro and in vivo activity against B-cell lymphomas and leukemias. The humanized variants of an original chimeric BAFF-R mAb retained BAFF-R binding affinity and antibody-dependent cellular cytotoxicity (ADCC) against a panel of human cell lines and primary lymphoma samples. Furthermore, 1 humanized BAFF-R mAb clone and its afucosylated version, glycoengineered to optimize the primary mechanism of action, prolonged survival of immunodeficient mice bearing human tumor cell lines or patient-derived lymphoma xenografts in 3 separate models, compared with controls. Finally, the tissue specificity of this humanized mAb was confirmed against a broad panel of normal human tissues. Taken together, we have identified a robust lead-candidate BAFF-R mAb for clinical development.
Inference about quantitative traits under selection: a Bayesian revisitation for the post-genomic era
Authors: Gianola Daniel , Fernando Rohan L. , Schön Chris C. 
Published: December 2022

Abstract
Background
Selection schemes distort inference when estimating differences between treatments or genetic associations between traits, and may degrade prediction of outcomes, e.g., the expected performance of the progeny of an individual with a certain genotype. If input and output measurements are not collected on random samples, inferences and predictions must be biased to some degree. Our paper revisits inference in quantitative genetics when using samples stemming from some selection process. The approach used integrates the classical notion of fitness with that of missing data. Treatment is fully Bayesian, with inference and prediction dealt with, in an unified manner. While focus is on animal and plant breeding, concepts apply to natural selection as well. Examples based on real data and stylized models illustrate how selection can be accounted for in four different situations, and sometimes without success.

Results
Our flexible “soft selection” setting helps to diagnose the extent to which selection can be ignored. The clear connection between probability of missingness and the concept of fitness in stylized selection scenarios is highlighted. It is not realistic to assume that a fixed selection threshold t holds in conceptual replication, as the chance of selection depends on observed and unobserved data, and on unequal amounts of information over individuals, aspects that a “soft” selection representation addresses explicitly. There does not seem to be a general prescription to accommodate potential distortions due to selection. In structures that combine cross-sectional, longitudinal and multi-trait data such as in animal breeding, balance is the exception rather than the rule. The Bayesian approach provides an integrated answer to inference, prediction and model choice under selection that goes beyond the likelihood-based approach, where breeding values are inferred indirectly.

Conclusions
The approach used here for inference and prediction under selection may or may not yield the best possible answers. One may believe that selection has been accounted for diligently, but the central problem of whether statistical inferences are good or bad does not have an unambiguous solution. On the other hand, the quality of predictions can be gauged empirically via appropriate training-testing of competing methods.
Genetic characteristics of colostrum refractive index and its use as a proxy for the concentration of immunoglobulins in Holstein cattle
Authors: Costa Angela , Visentin Giulio , Goi Arianna , De Marchi Massimo , Penasa Mauro 
Published: December 2022

Abstract
Background
Colostral concentration of immunoglobulins (Ig) is crucial for the passive transfer of antibodies from the cow to the new-born calf. Direct determination of Ig by the gold standard radial immunodiffusion method is demanding in terms of time and costs. For this reason, a refractometer is commonly used at the farm level for an indirect estimation of colostrum quality, which is given as the Ig concentration. In this study, colostrum samples were collected from 548 Italian Holstein cows within 6 h of calving. The refractive index (BRIX, %) of these samples was assessed using a portable optical refractometer, as well as the concentration of total protein, IgG, IgA, and IgM by radial immunodiffusion. A four-trait animal model was used to estimate genetic parameters for BRIX and the different immunoglobulin isotypes. A receiver operating characteristic analysis was carried out to evaluate the BRIX diagnostic accuracy.

Results
Colostral BRIX was moderately heritable (0.26) and its genetic and phenotypic correlations with IgG (0.91, 0.78), IgA (0.57, 0.57), and IgM (0.71, 0.61) were all positive and of similar order, although the genetic correlations were generally higher than the phenotypic correlations. Low-quality colostrum samples, defined as those with an IgG concentration lower than 50 g/L, were accurately identified by the refractive index on the BRIX scale, with an area under the curve of 0.90.

Conclusions
The use of a refractometer is recommended on dairy farms to produce a proxy for colostral Ig concentration. BRIX is a useful phenotyping tool that can be used in cattle to improve the quality of colostrum for first feeding of calves through both traditional genetic and genomic strategies. Improving colostrum quality will reduce the incidence of failure of passive transfer of immunity in young stock.
De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)
Authors: Linscott T. Mason , González-González Andrea , Hirano Takahiro , Parent Christine E. 
Published: December 2022

Abstract
Background
Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO3), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species.

Results
Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2–3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome.

Conclusions
Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs.
Leaf transcriptome analysis of Medicago ruthenica revealed its response and adaptive strategy to drought and drought recovery
Authors: Wu Rina , Xu Bo , Shi Fengling 
Published: December 2022

Abstract
Background
Drought is one of the main causes of losses in forage crop yield and animal production. Medicago ruthenica (L.) cv. Zhilixing is a high-yielding alfalfa cultivar also known for its high tolerance to drought. We analyzed the transcriptome profile of this cultivar throughout drought stress and recovery and we were able to describe its phased response through the expression profiles of overlapping gene networks and drought-specific genes.

Results
The ABA and auxin signal transduction pathways are overlapping pathways in response to drought and drought recovery in forage crops. Medicago ruthenica (L.) cv. Zhilixing adopts different strategies at different degrees of drought stress. On the 9th day of drought, transcriptional regulations related to osmoregulation are enhanced mainly through increased activities of carbohydrate and amino acid metabolism, while photosynthetic activities were reduced to slow down growth. With drought prolonging, on the 12th day of drought, the synthesis of proline and other stored organic substances was suppressed in general. After recovery, Medicago ruthenica synthesizes flavonoids through the flavonoid biosynthesis pathway to remove accumulated ROS and repair the oxidative damage from water stress. In addition, the regulation of circadian rhythm seems to accelerate the drought recovery process.

Conclusions
Medicago ruthenica adapts to drought by regulating the osmoregulatory system and photosynthesis, which appears to involve the ABA and auxin signaling pathways as key regulators. Furthermore, the synthesis of flavonoids and the regulation of the circadian rhythm can accelerate the recovery process. These results enriched our knowledge of molecular responses to drought and drought recovery in Medicago ruthenica and provide useful information for the development of new legume forage grass varieties with improved adaptability to drought stress.