bluuebunny/crossref_metadata_2025 huggingface dataset:
Micro electrical discharge drilling in SS304 and its multiparameter optimization using desirability function analysis
Authors: Majumder Tanmoy , Kebede Alemu Workie , Patowari Promod Kumar , Sahoo Chinmaya Kumar
Published: June 2024

The present investigation examines the use of micro-electrical discharge machining (μEDM) for microhole drilling in stainless steel grade 304. In this experiment, a Taguchi L18 orthogonal array is considered with four process parameters, viz. capacitance, voltage, feed rate and tool rotation. Material removal rate and microhole precision, such as circularity, overcut, and taperness, have been studied to assess machinability. Parametric variation of response measures with process variables are studied and their corresponding impacts are calculated using ANOVA. Desirability function analysis (DFA) is selected to optimize the process parameter for the best possible response and most desirable condition of the experiment, and results show an improvement in overall desirability by 10.47% at optimum parameter settings of capacitance = 103pF, voltage = 150 V, feed rate = 20 μm sec−1 and tool rotation = 2800 rpm.
The effect of prior austenite grain size on crystallography and variant selection in carbide-free nano-structured bainite
Authors: Chhajed Bhawesh , Singh Kritika , Singh Aparna
Published: June 2024

Prior austenite grain size (PAGS) significantly affects the microstructure and in turn the mechanical properties of nano-structured bainite. In this study, information about crystallographic variants/blocks as well as packets has been extracted using electron backscattered diffraction (EBSD) technique for two blocks of nano-baintic steels with different PAGS obtained by austenitization at two different temperatures of 900°C and 1000°C respectively. However, the bainitic fraction has been maintained to be similar by choosing the same isothermal temperature of 250°C for transformation to bainite. The child-parent orientation relationship (OR) was determined to be close to Kurdjumov-Sachs (K-S) using EBSD for larger PAGS specimen while smaller PAGS specimen displayed closeness to K-S OR predominantly and Nishiyama-Wassermann (N-W) OR in some regions. It was observed that a higher PAGS leads to finer bainitic lath thickness, packet size and block width size. Stricter variant selection was found in smaller PAGS sample even though variant pairing was observed between variants of higher misorientation. This hints towards small number of nucleation sites for a grain and space constraint, rather than the tendency for pairing as the reason for selection.
Causal hybrid modeling with double machine learning—applications in carbon flux modeling
Authors: Cohrs Kai-Hendrik , Varando Gherardo , Carvalhais Nuno , Reichstein Markus , Camps-Valls Gustau
Published: June 2024

Hybrid modeling integrates machine learning with scientific knowledge to enhance interpretability, generalization, and adherence to natural laws. Nevertheless, equifinality and regularization biases pose challenges in hybrid modeling to achieve these purposes. This paper introduces a novel approach to estimating hybrid models via a causal inference framework, specifically employing double machine learning (DML) to estimate causal effects. We showcase its use for the Earth sciences on two problems related to carbon dioxide fluxes. In the Q
10 model, we demonstrate that DML-based hybrid modeling is superior in estimating causal parameters over end-to-end deep neural network approaches, proving efficiency, robustness to bias from regularization methods, and circumventing equifinality. Our approach, applied to carbon flux partitioning, exhibits flexibility in accommodating heterogeneous causal effects. The study emphasizes the necessity of explicitly defining causal graphs and relationships, advocating for this as a general best practice. We encourage the continued exploration of causality in hybrid models for more interpretable and trustworthy results in knowledge-guided machine learning.
Extremal Kähler-Ricci solitons on Fano homogeneous toric bundles
Authors: Lian Zhao
Published: June 2024

In this short note, we prove that an extremal Kähler-Ricci soliton on a Fano homogeneous toric bundle is Kähler-Einstein.
A universal Kaluzhnin–Krasner embedding theorem
Authors: Deval Bo , García-Martínez Xabier , Van der Linden Tim
Published: June 2024

Given two groups

A
A

and

B
B

, the Kaluzhnin–Krasner universal embedding theorem states that the wreath product

A
≀
B

A\wr B

acts as a universal receptacle for extensions from

A
A

to

B
B

. For a split extension, this embedding is compatible with the canonical splitting of the wreath product, which is further universal in a precise sense. This result was recently extended to Lie algebras and to cocommutative Hopf algebras.

The aim of the present article is to explore the feasibility of adapting the theorem to other types of algebraic structures. By explaining the underlying unity of the three known cases, our analysis gives necessary and sufficient conditions for this to happen.

From those we may for instance conclude that a version for crossed modules can indeed be attained, while the theorem cannot be adapted to, say, associative algebras, Jordan algebras or Leibniz algebras, when working over an infinite field: we prove that then, amongst non-associative algebras, only Lie algebras admit a universal Kaluzhnin–Krasner embedding theorem.
Regularity of the Siciak-Zaharjuta extremal function on compact Kähler manifolds
Authors: Nguyen Ngoc Cuong
Published: June 2024

We prove that the regularity of the extremal function of a compact subset of a compact Kähler manifold is a local property, and that the continuity and Hölder continuity are equivalent to classical notions of the local

L
L

-regularity and the locally Hölder continuous property in pluripotential theory. As a consequence we give an effective characterization of the

(

C

α

,

C

α
′

)

(\mathscr {C}^\alpha , \mathscr {C}^{\alpha ’})

-regularity of compact sets, the notion introduced by Dinh, Ma and Nguyen [Ann. Sci. Éc. Norm. Supér. (4) 50 (2017), pp. 545–578]. Using this criterion all compact fat subanalytic sets in

R

n

\mathbb {R}^n

are shown to be regular in this sense.
Llarull type theorems on complete manifolds with positive scalar curvature
Authors: Hao Tianze , Shi Yuguang , Sun Yukai
Published: June 2024

In this paper, without assuming that manifolds are spin, we prove that if a compact orientable, and connected Riemannian manifold

(

M

n

,
g
)

(M^{n},g)

with scalar curvature

R

g

≥
6

R_{g}\geq 6

admits a non-zero degree and

1
1

-Lipschitz map to
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis double-struck upper S cubed times double-struck upper T Superscript n minus 3 Baseline comma g Subscript double-struck upper S cubed Baseline plus g Subscript double-struck upper T Sub Superscript n minus 3 Subscript Baseline right-parenthesis">

(

S

3

×

T

n
−
3

,

g

S

3

+

g

T

n
−
3

)

(\mathbb {S}^{3}\times \mathbb {T}^{n-3},g_{\mathbb {S}^{3}}+g_{\mathbb {T}^{n-3}})

, for

4
≤
n
≤
7

4\leq n\leq 7

, then

(

M

n

,
g
)

(M^{n},g)

is locally isometric to

S

3

×

T

n
−
3

\mathbb {S}^{3}\times \mathbb {T}^{n-3}

. Similar results are established for non-compact cases as
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis double-struck upper S cubed times double-struck upper R Superscript n minus 3 Baseline comma g Subscript double-struck upper S cubed Baseline plus g Subscript double-struck upper R Sub Superscript n minus 3 Subscript Baseline right-parenthesis">

(

S

3

×

R

n
−
3

,

g

S

3

+

g

R

n
−
3

)

(\mathbb {S}^{3}\times \mathbb {R}^{n-3},g_{\mathbb {S}^{3}}+g_{\mathbb {R}^{n-3}})

being model spaces. We observe that the results differ significantly when

n
=
4

n=4

compared to

n
≥
5

n\geq 5

. Our results imply that the

ϵ
\epsilon

-gap length extremality of the standard

S

3

\mathbb {S}^3

is stable under the Riemannian product with

R

m

\mathbb {R}^m

,

1
≤
m
≤
4

1\leq m\leq 4

(see

D

3

D_{3}

. Question in Gromov’s paper [Foundations of mathematics and physics one century after Hilbert, Spring, Cham, 2018, p. 153]).
Frobenius-Poincaré function and Hilbert-Kunz multiplicity
Authors: Mukhopadhyay Alapan
Published: June 2024

We generalize the notion of Hilbert-Kunz multiplicity of a graded triple

(
M
,
R
,
I
)

(M,R,I)

in characteristic

p
>
0

p>0

by proving that for any complex number

y
y

, the limit
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="limit Underscript n right-arrow normal infinity Endscripts left-parenthesis StartFraction 1 Over p Superscript n Baseline EndFraction right-parenthesis Superscript dimension left-parenthesis upper M right-parenthesis Baseline sigma-summation Underscript j equals negative normal infinity Overscript normal infinity Endscripts lamda left-parenthesis left-parenthesis StartFraction upper M Over upper I Superscript left-bracket p Super Superscript n Superscript right-bracket Baseline upper M EndFraction right-parenthesis Subscript j Baseline right-parenthesis e Superscript minus i y j slash p Super Superscript n">

lim

n
→
∞

(

1

p
n

)

dim
⁡
(
M
)

∑

j
=
−
∞

∞

λ

(
(

M

I

[

p
n

]

M

)
j

)

e

−
i
y
j

/

p
n

\begin{equation*} \underset {n \to \infty }{\lim }(\frac {1}{p^n})^{\operatorname {dim}(M)}\sum \limits _{j= -\infty }^{\infty }\lambda \left ( (\frac {M}{I^{[p^n]}M})_j\right )e^{-iyj/p^n} \end{equation*}

exists. We prove that the limiting function in the complex variable

y
y

is entire and name this function the Frobenius-Poincaré function. We establish various properties of Frobenius-Poincaré functions including its relation with the tight closure of the defining ideal

I
I

; and relate the study Frobenius-Poincaré functions to the behaviour of graded Betti numbers of

R

I

[

p
n

]

\frac {R}{I^{[p^n]}}

as

n
n

varies. Our description of Frobenius-Poincaré functions in dimension one and two and other examples raises questions on the structure of Frobenius-Poincaré functions in general.
A proof of the Lewis-Reiner-Stanton conjecture for the Borel subgroup
Authors: Ha Le Minh , Dang Ho Hai Nguyen , Van Nghia Nguyen
Published: June 2024

For each parabolic subgroup

P

\mathrm {P}

of the general linear group

GL
n

⁡
(

F

q

)

\operatorname {GL}_n(\mathbb {F}_q)

, a conjecture due to Lewis, Reiner and Stanton [Proc. Roy. Soc. Edinburgh Sect. A 147 (2017), pp. 831–873] predicts a formula for the Hilbert series of the space of invariants

Q

m

(
n

)

P

\mathcal {Q}_m(n)^\mathrm {P}

where

Q

m

(
n
)

\mathcal {Q}_m(n)

is the quotient ring
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="double-struck upper F Subscript q Baseline left-bracket x 1 comma ellipsis comma x Subscript n Baseline right-bracket slash left-parenthesis x 1 Superscript q Super Superscript m Superscript Baseline comma ellipsis comma x Subscript n Superscript q Super Superscript m Superscript Baseline right-parenthesis">

F

q

[

x
1

,
…
,

x
n

]

/

(

x
1

q
m

,
…
,

x
n

q
m

)

\mathbb {F}_q[x_1,\ldots ,x_n]/(x_1^{q^m},\ldots ,x_n^{q^m})

. In this paper, we prove the conjecture for the Borel subgroup

B

\mathrm {B}

by constructing a linear basis for

Q

m

(
n

)

B

\mathcal {Q}_m(n)^\mathrm {B}

. The construction is based on an operator

δ
\delta

which produces new invariants from old invariants of lower ranks. We also upgrade the conjecture of Lewis, Reiner and Stanton by proposing an explicit basis for the space of invariants for each parabolic subgroup.
Fiber-type prebiotics and gynecological and breast cancers risk: the PrebiotiCa study
Authors: Turati Federica , Esposito Giovanna , Concina Federica , Fiori Federica , Parpinel Maria , Parazzini Fabio , Crispo Anna , Negri Eva , Serraino Diego , La Vecchia Carlo
Published: June 2024

Prebiotics may influence the risk of hormone-related female cancers by modulating the gut microbiota involved in estrogen metabolism. We evaluated the association of fiber-type prebiotic intake with breast, endometrial, and ovarian cancers. Data derived from a network of Italian hospital-based case-control studies (1991-2006), including 2560 cases of cancer of the breast (n = 2588 control participants), 454 of the endometrium (n = 908 control participants), and 1031 of the ovary (n = 2411 control participants). Inulin-type fructans and selected fructo-oligosaccharides (namely, nystose, kestose, and 1F-β-fructofuranosylnystose) and galacto-oligosaccharides (namely, raffinose and stachyose) were quantified in food products via laboratory analyses. Prebiotic intake was estimated by multiplying intake according to food frequency questionnaire responses by the foods’ prebiotic content. Odds ratios (ORs) and the corresponding 95% CIs were derived by multiple logistic regression models. Nystose intake was marginally directly associated with breast (for quartile 4 vs quartile 1: OR = 1.20; 95% CI, 1.00-1.45), ovarian (OR = 1.39; 95% CI, 1.04-1.84), and endometrial (OR = 1.32; 95% CI, 0.85-2.03) cancer risk. High amounts of 1F-β-fructofuranosylnystose intake were inversely associated with ovarian cancer (OR = 0.67; 95% CI, 0.52-0.85). Inulin-type fructans, kestose, raffinose, and stachyose were not associated with the 3 cancers. The intake of most fiber-type prebiotics was not appreciably and consistently associated with breast, endometrial, and ovarian cancer risks.

This article is part of a Special Collection on Gynecological Cancer.
Population attributable fraction of total stroke associated with modifiable risk factors in the United States
Authors: Lee Mark , Lakshminarayan Kamakshi , Sedaghat Sanaz , Sabayan Behnam , Chen Lin Yee , Johansen Michelle C , Gottesman Rebecca F , Heckbert Susan R , Misialek Jeffrey R , Szklo Moyses , Lutsey Pamela L
Published: June 2024

Stroke is a leading cause of death in the United States across all race/ethnicity and sex groups, though disparities exist. We investigated the potential for primary prevention of total first stroke for Americans aged 20 years or older, stratified by sex and race/ethnicity. Specifically, we calculated population attributable fractions (PAFs) of first stroke for 7 potentially modifiable risk factors: smoking, physical inactivity, poor diet, obesity, hypertension, diabetes, and atrial fibrillation. Population attributable fractions are a function of (1) the relative risk of first stroke for people with the exposure and (2) the prevalence of the risk factor in the population. Relative risks came from recent meta-analyses, and sex- and race/ethnicity–specific prevalence estimates came from the 2015-2018 National Health and Nutrition Examination Survey or Multi-Ethnic Study of Atherosclerosis (for atrial fibrillation only). Approximately one-third of strokes (35.7% [95% CI, 21.6-49.0] for women; 32.7% [95% CI, 19.2-45.1] for men) were attributable to the 7 risk factors we considered. A 20% proportional reduction in stroke risk factors would result in approximately 37 000 fewer strokes annually in the United States. The estimated PAF was highest for non-Hispanic Black women (39.3%; 95% CI, 24.8-52.3) and lowest for non-Hispanic Asian men (25.5%; 95% CI, 14.6-36.2). For most groups, obesity and hypertension were the largest contributors to stroke rates.
Please Walk on This: Gutai and the Emergence of Walkable Art
Authors: Tymkiw Michael
Published: June 2024

This essay traces the emergence of ‘walkable art’, a term used to describe works of fine art made to be walked on by audiences. Focusing on the two earliest examples of such works, created respectively by Gutai artists Shōzō Shimamoto and Akira Kanayama in 1955 and 1956, it argues that the rise of walkable art evinced an attempt to mediate the reconstruction of human subjectivity in postwar Japan through a close engagement with bipedalism. By offering a new model for conceptualising a spectator’s relationship to ground-based works, the category of walkable art that emerged in mid-1950s Japan challenges canonical, Euroamerican-centric narratives of horizontality. It also attests to the expanded interest among postwar artists from the Americas, Asia and Europe in using the ground to develop new approaches for displaying and experiencing art.
DEAttentionDTA: protein–ligand binding affinity prediction based on dynamic embedding and self-attention
Authors: Chen Xiying , Huang Jinsha , Shen Tianqiao , Zhang Houjin , Xu Li , Yang Min , Xie Xiaoman , Yan Yunjun , Yan Jinyong
Published: June 2024

Motivation

Predicting protein–ligand binding affinity is crucial in new drug discovery and development. However, most existing models rely on acquiring 3D structures of elusive proteins. Combining amino acid sequences with ligand sequences and better highlighting active sites are also significant challenges.

Results

We propose an innovative neural network model called DEAttentionDTA, based on dynamic word embeddings and a self-attention mechanism, for predicting protein–ligand binding affinity. DEAttentionDTA takes the 1D sequence information of proteins as input, including the global sequence features of amino acids, local features of the active pocket site, and linear representation information of the ligand molecule in the SMILE format. These three linear sequences are fed into a dynamic word-embedding layer based on a 1D convolutional neural network for embedding encoding and are correlated through a self-attention mechanism. The output affinity prediction values are generated using a linear layer. We compared DEAttentionDTA with various mainstream tools and achieved significantly superior results on the same dataset. We then assessed the performance of this model in the p38 protein family.

Availability and implementation

The resource codes are available at https://github.com/whatamazing1/DEAttentionDTA.
Approximation algorithms for maximum weighted internal spanning trees in regular graphs and subdivisions of graphs
Authors: Hakim Sheikh Azizul , Nishat Rahnuma Islam , Rahman Md Saidur
Published: June 2024

Let $G$ be a vertex-weighted connected graph of $n$ vertices and let $T$ be a spanning tree of $G$. We call $T$ a maximum weighted internal spanning tree of $G$ if the sum of the weights of the internal vertices of $T$ is the maximum over all spanning trees of $G$. The maximum weighted internal spanning tree (MaxwIST) problem asks to find such a spanning tree $T$ of $G$. The problem is NP-hard. We give an $O(dn)$ time approximation algorithm for $d$-regular graphs of $n=|V|$ vertices that computes a spanning tree with total weight of the internal vertices is at least $\frac{\beta _{d}}{\beta _{d} +d-2} - \epsilon $ of the total weight of all the vertices of the graph for any $\epsilon>0$, where $\beta _{d} = (d-1)H_{d-1}$, and $H_{d-1} = \sum _{i=1}^{d-1} i^{-1}$ is the $(d-1)$th harmonic number. For every $d \geq 3$ and $n_{0} \geq 1$, we show the construction of a $d$-regular graph of at least $n_{0}$ vertices, such that for any of its spanning trees, $\frac{w(I)}{w(V)}\le \frac{d}{d+1}$ holds. We give an $O(dn)$ time approximation algorithm for subdivisions of $d$-regular graphs, where the ratio of the internal weight of the spanning tree with the total vertex weight of the graph is at least $\frac{d-1}{2d-3} - \epsilon $ for $\epsilon>0$. We extend our study to $x$-subdivisions of Hamiltonian and hypoHamiltonian graphs, where each edge of the original Hamiltonian or hypoHamiltonian graph has been subdivided at least $x$ times. For those two graph classes, we show that there exists a spanning tree with internal vertex weight at least $1-\frac{2}{x-1}$ of the total vertex weight of the graph. Furthermore, we give $O(n)$ time algorithm for $x$-subdivisions of biconnected outerplanar graphs and $4$-connected planar graphs to achieve the above bound.
Novel metagenomics analysis of stony coral tissue loss disease
Authors: Heinz Jakob M , Lu Jennifer , Huebner Lindsay K , Salzberg Steven L , Sommer Markus , Rosales Stephanie M
Published: June 2024

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset.
Stem lodging Resistance-1 controls stem strength by positively regulating the biosynthesis of cell wall components in Capsicum annuum L.
Authors: Li Qing , Fu Canfang , Yang Bozhi , Yu Huiyang , He Huan , Xu Qing , Miao Wu , Liu Rongyun , Chen Wenchao , Zhang Zhuqing , Zou Xuexiao , Hu Bowen , Ou Lijun
Published: June 2024

Lodging presents a significant challenge in cultivating high-yield crops with extensive above-ground biomass, yet the molecular mechanisms underlying this phenomenon in the Solanaceae family remain largely unexplored. In this study, we identified a gene, CaSLR1 (Capsicum annuum Stem Lodging Resistance 1), which encodes a MYELOBLASTOSIS (MYB) family transcription factor, from a lodging-affected C. annuum EMS mutant. The suppression of CaSLR1 expression in pepper led to notable stem lodging, reduced thickness of the secondary cell wall, and decreased stem strength. A similar phenotype was observed in tomato with the knockdown of SlMYB61, the orthologous gene to CaSLR1. Further investigations demonstrated that CaNAC6, a gene involved in secondary cell wall (SCW) formation, is co-expressed with CaSLR1 and acts as a positive regulator of its expression, as confirmed through yeast one-hybrid, dual-luciferase reporter assays, and electrophoretic mobility shift assays. These findings elucidate the CaNAC6-CaSLR1 module that contributes to lodging resistance, emphasizing the critical role of CaSLR1 in the lodging resistance regulatory network.
Advances in understanding the graft healing mechanism: a review of factors and regulatory pathways
Authors: Wang Lixian , Liao Yangmei , Liu Jiming , Zhao Tianyun , Jia Liming , Chen Zhong
Published: June 2024

Grafting is a widely used technique for asexual plant reproduction, especially in agriculture and forestry. This procedure is used to shorten the seedling period, improve the structure of scion branches, and help plants adapt to difficult environments. Although grafting has numerous benefits, several obstacles remain to be overcome. The connection between scion and rootstock is regulated by various factors, including phytohormones and molecular mechanisms, which are crucial for graft healing. This review provides an overview of recent advances in the field of grafting, with a specific focus on the factors and regulatory pathways that influence graft healing. The ultimate goal is to aid understanding of how to achieve successful grafting between plants and create desirable grafting chimeras. We provide an overview of the latest developments in plant grafting, covering aspects related to morphology, physiology, and molecular biology. We also discuss research directions in polyploid breeding and long-distance transfer of small molecules in grafted plants.
Imaginary Quadratic Fields With ℓ-Torsion-Free Class Groups and Specified Split Primes
Authors: Beckwith Olivia , Raum Martin , Richter Olav K
Published: June 2024

Given an odd prime $\ell $ and finite set of odd primes $S_{+}$, we prove the existence of an imaginary quadratic field whose class number is indivisible by $\ell $ and which splits at every prime in $S_{+}$. Notably, we do not require that $p \not \equiv -1 \,\;(\mathrm{mod}\, \ell )$ for any of the split primes $p$ that we impose. Our theorem is in the spirit of a result by Wiles, but we introduce a new method. It relies on a significant improvement of our earlier work on the classification of non-holomorphic Ramanujan-type congruences for Hurwitz class numbers.
Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique
Authors: Man DeDe Kwun Wai , Hermans Syrie M , Taubert Martin , Garcia Sarahi L , Hengoju Sundar , Küsel Kirsten , Rosenbaum Miriam A
Published: June 2024

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.
Rhizosphere-xylem sap connections in the olive tree microbiome: implications for biostimulation approaches
Authors: Marques Mónica , Sierra-Garcia I Natalia , Leitão Frederico , Martins João , Patinha Carla , Pinto Glória , Cunha Ângela
Published: June 2024

Aims

Climate change is endangering olive groves. Farmers are adapting by exploring new varieties of olive trees and examining the role of microbiomes in plant health.

The main objectives of this work were to determine the primary factors that influence the microbiome of olive trees and to analyze the connection between the rhizosphere and endosphere compartments.

Methods and Results

The rhizosphere and xylem sap microbiomes of two olive tree varieties were characterized by next-generation 16S rRNA amplicon sequencing, and soil descriptors were analyzed. Bacterial communities in the rhizosphere of olive trees were more diverse than those found in the xylem sap. Pseudomonadota, Actinobacteriota, Acidobacteriota, and Bacillota were the dominant phyla in both compartments. At the genus level, only very few taxa were shared between soil and sap bacterial communities.

Conclusions

The composition of the bacteriome was more affected by the plant compartment than by the olive cultivar or soil properties, and a direct route from the rhizosphere to the endosphere could not be confirmed. The large number of plant growth-promoting bacteria found in both compartments provides promising prospects for improving agricultural outcomes through microbiome engineering.
Effect of repeated HPA axis stimulation on hair cortisol concentration, growth, and behavior in preweaned dairy cattle
Authors: Kern Jessica , Jorgensen Matthew W , Boerman Jacquelyn P , Erasmus Marisa , Johnson Jay S , Pempek Jessica A
Published: June 2024

The study objective was to investigate the effect of repeated hypothalamic–pituitary–adrenal (HPA) axis stimulation using synthetic adrenocorticotropic hormone (ACTH) intramuscular injections on hair cortisol concentration, growth, and behavior in preweaned dairy calves. Twenty-seven Holstein calves were assigned to nine triads (based on sex and birth order) and randomly assigned to 1 of 3 treatments: 1) control (CON; 2 mL saline weekly); 2) moderate (MOD; alternating Cosyntropin [2 mcg/kg body weight (BW)] and saline weekly); or 3) frequent (FREQ; Cosyntropin [2 mcg/kg BW] weekly). Calves received their first injection on study day 0 (7 ± 1 d of age). Hair was collected from the tail switch between days −5 and −3 (baseline), 21, and 49 and analyzed for cortisol concentration. To verify the endogenous cortisol release by Cosyntropin during the treatment period, saliva was collected on days 0, 14, 28, and 42 before injection and every 15 min for 2 h after injection for analysis of salivary cortisol concentration. Calves were fitted with accelerometers to continuously monitor lying time, number of lying bouts, and lying bout duration throughout the study. Growth measures (BW, hip height, hip width) were recorded weekly. Data were analyzed using repeated measures ANOVA (SAS, Version 9.4), and models included the fixed effects of treatment, time (min or study day), and interaction between treatment and time. Temperature humidity index was included as a continuous covariate in all models. We observed a treatment × min interaction (P < 0.0001), whereby salivary cortisol concentration was lower in CON calves compared to MOD and FREQ calves 15 to 120 min postinjection. While hair cortisol concentration was not influenced by treatment, concentration decreased from day 21 (1.28 ± 0.03 ng/mL) to 49 (0.93 ± 0.03 ng/mL). Average BW was similar across treatments (CON [59.4 ± 1.09 kg], MOD [58.6 ± 0.98 kg], and FREQ [57.6 ± 0.96 kg]; P = 0.50). There was no evidence to suggest a difference in average daily lying time (CON [18.5 ± 0.23 h/d], MOD [18.6 ± 0.23 h/d], and FREQ [18.5 ± 0.23 h/d]; P = 0.99). These results suggest that repeated HPA axis stimulation through Cosyntropin administration increased salivary cortisol concentration, but did not influence hair cortisol concentration, growth, or behavior in preweaned dairy calves.
The neurodevelopmental genes alan shepard and Neuroglian contribute to female mate preference in African Drosophila melanogaster
Authors: Roy Paula R , Castillo Dean M
Published: June 2024

Mate choice is a key trait that determines fitness for most sexually reproducing organisms, with females often being the choosy sex. Female preference often results in strong selection on male traits that can drive rapid divergence of traits and preferences between lineages, leading to reproductive isolation. Despite this fundamental property of female mate choice, very few loci have been identified that contribute to mate choice and reproductive isolation. We used a combination of population genetics, quantitative complementation tests, and behavioural assays to demonstrate that alan shepard and Neuroglian contribute to female mate choice, and could contribute to partial reproductive isolation between populations of Drosophila melanogaster. Our study is among the first to identify genes that contribute to female mate preference in this historically important system, where female preference is an active premating barrier to reproduction. The identification of loci that are primarily known for their roles in neurodevelopment provides intriguing questions of how female mate preference evolves in populations via changes in sensory system and higher learning brain centres.
Determining the accuracy and suitability of common analytical techniques for sophorolipid biosurfactants
Authors: Ingham Benjamin , Sung Rehana , Kay Phil , Hollywood Katherine , Wongsirichot Phavit , Veitch Alistair , Winterburn James
Published: June 2024

To determine the performance of a sophorolipid biosurfactant production process, it is important to have accurate and specific analytical techniques in place. Among the most popular are the anthrone assay, gravimetric quantification (hexane:ethyl acetate extraction), and high-performance liquid chromatography (HPLC). The choice of analytical tool varies depending on cost, availability, and ease of use; however, these techniques have never been compared directly against one another. In this work, 75 fermentation broths with varying product/substrate concentrations were comprehensively tested with the 3 techniques and compared. HPLC–ultraviolet detection (198 nm) was capable of quantifying C18:1 subterminal hydroxyl diacetylated lactonic sophorolipid down to a lower limit of 0.3 g/L with low variability (<3.21%). Gravimetric quantification of the broths following liquid:liquid extraction with hexane and ethyl acetate showed some linearity (R2 = .658) when compared to HPLC but could not quantify lower than 11.06 g/L, even when no sophorolipids were detected in the sample, highlighting the non-specificity of the method to co-extract non-sophorolipid components in the final gravimetric measure. The anthrone assay showed no linearity (R2 = .129) and was found to cross-react with media components (rapeseed oil, corn steep liquor, glucose), leading to consistent overestimation of sophorolipid concentration. The appearance of poor biomass separation during sample preparation with centrifugation was noted and resolved with a novel sample preparation method with pure ethanol. Extensive analysis and comparisons of the most common sophorolipid quantification techniques are explored and the limitations/advantages are highlighted. The findings provide a guide for scientists to make an informed decision on the suitable quantification tool that meets their needs, exploring all aspects of the analysis process from harvest, sample preparation, and analysis.
Glioblastoma vulnerability to neddylation inhibition is dependent on PTEN status, and dysregulation of the cell cycle and DNA replication
Authors: Taylor Brett , Tang Nanyun , Hao Yue , Lee Matthew , Peng Sen , Bybee Rita , Hartman Lauren , Garcia-Mansfield Krystine , Sharma Ritin , Pirrotte Patrick , Ma Jianhui , Parisian Alison D , Furnari Frank , Dhruv Harshil D , Berens Michael E
Published: June 2024

Background

Neddylation (NAE) inhibition, affecting posttranslational protein function and turnover, is a promising therapeutic approach to cancer. We report the cytotoxic vulnerability to NAE inhibitors in a subset of glioblastoma (GBM) preclinical models and identify genetic alterations and biological processes underlying differential response.

Methods

GBM DNA sequencing and transcriptomic data were queried for genes associated with response to NAE inhibition; candidates were validated by molecular techniques. Multi-omics and functional assays revealed processes implicated in NAE inhibition response.

Results

Transcriptomics and shotgun proteomics depict PTEN signaling, DNA replication, and DNA repair pathways as significant differentiators between sensitive and resistant models. Vulnerability to MLN4924, a NAE inhibitor, is associated with elevated S-phase populations, DNA re-replication, and DNA damage. In a panel of GBM models, loss of WT PTEN is associated with resistance to different NAE inhibitors. A NAE inhibition response gene set could segregate the GBM cell lines that are most resistant to MLN4924.

Conclusions

Loss of WT PTEN is associated with non-sensitivity to 3 different compounds that inhibit NAE in GBM. A NAE inhibition response gene set largely consisting of DNA replication genes could segregate GBM cell lines most resistant to NAEi and may be the basis for future development of NAE inhibition signatures of vulnerability and clinical trial enrollment within a precision medicine paradigm.
Racialization in the Early Modern Period
Authors: Mejia-LaPerle Carol , Mendoza Kirsten , Kafantaris Mira 'Assaf , Grier Miles , Weissbourd Emily , Dadabhoy Ambereen , Adams Brandi , Sarkar Debapriya
Published: June 2024

Race is an ideological fiction embedded in material realities. It is a collective operation and an individual experience. Race is a factor in the formation of gender, class, sexuality, religion, politics, economics, philosophy, and subjectivity because of its capacious involvement in all facets of social life. And yet race is also, in this article, uniquely important to understanding the people, events, and artifacts of the Renaissance and Reformation. Mired in these paradoxes, the study of race in early modernity requires multidisciplinary approaches, transhistorical awareness, and a protean vocabulary to analyze the discourses of race, the means of racialization, and the consequences of racism. Because scholarship on race should also strive to be anti-racist, this article is an inclusive, diverse, justice-oriented, collective effort. Entries reflect the innovations in methodologies and the range of materials that have established the importance of the topic despite the absence and alterity plaguing the archived histories of racial construction. It is worth noting that the decades-long race scholarship featured in this article reckoned with not only the challenges of archival silences but also the obstacles set by academic institutions that suppressed, undermined, and denied the significance of racial thinking to early moderns. Showing the ways that racialized groups were cultural influences and active participants in the Renaissance and Reformation, multi-authored sections prove the widespread social impact of English engagements with, and representations of, racial subjects in theaters, in classrooms, in royal courts, and in everyday life. The article also tackles racial operations beyond England in discussions of, for instance, religion in the Islamic world, theatrical practices on the Continent, and cross-cultural engagements in a global economy. Future considerations in disciplines such as book history, education, science, and ecocriticism expand the implications of this scholarship in recovering the past and showing the relevance of the recovery. Underwriting all aspects of race in the period are the dehumanizing agendas of the slave trade, the violences of forced diaspora, and the theft of Indigenous peoples’ lands and resources. Race is not a coherent system or a stable epistemology; rather, its operations and expressions are repeated, reiterated, and reinvented in the context of social and cultural histories. The entries convey these social and cultural histories by providing an overview of the theoretical scaffolds for and significant findings on racialization in the Early Modern period. This section is contributed by Carol Mejia LaPerle.
Islamic Traditions and Yoga
Authors: D'Silva Patrick
Published: June 2024

The subject of Muslim engagement with yoga is challenging and enlightening for several key reasons. First, the primary and secondary sources listed below document the extended and multifaceted history of Muslim engagement with yoga. For historical reasons the majority of the sources below focus on the history of Muslims and yogis (sometimes written as jogis) in South Asia, almost all of which took place long before Partition. This complicates modern perceptions that members of one religious community automatically and casually eschew or actively reject anything associated with other religious groups. Second, this field of study holds great—and as of yet largely unrealized—potential for scholars looking to reconstruct mysticism as a bodily practice in which the bodies involved are understood as commensurate with one another. This means that the people who authored, translated, and interpreted the primary sources under examination did not see “Muslim” and “Hindu” bodies as quintessentially different from one another. With appropriate training, anyone can use these techniques to access whatever powers may be promised, whether they are of use on a daily level or in the more ultimate sense of yoking the mind and body together to experience some type of liberation of the soul from samsara, the cycle of reincarnation. In so doing, one understands yoga as yet another technology of the (esoteric) self. Importantly, Muslim engagement with yoga involves confronting moments of incommensurability, such as translating terms like samsara, for example, linguistically (from Sanskrit into Persian, but also conceptually from Hinduism to Islam). Third, the available sources—whether from the premodern or modern periods—actively challenge the claim made by present-day Hindu nationalists that yoga is uniquely Hindu, or even Indian. Yoga is undeniably part Hinduism, but these techniques come to be deployed by other religious traditions (such as Buddhism and Jainism). The sources below demonstrate the extent to which these philosophies and techniques were considered important enough to integrate within the growing field of Islamicate sciences, especially as evidenced by Persian encyclopedias compiled from the fourteenth century ce onward. It is important to understand yoga in this sense as a multifaceted phenomenon that goes beyond modern postural practice and includes philosophical inquiry into the nature of existence. How do the techniques expressed by yogis compare with those by Sufis (Muslim mystics)? What types of translation strategies were developed? How does the texture of these inquiries change from South Asia to Persia, and (relevant for the modern period) when the Euro-American academy becomes involved? This subject holds great value for general observers and scholars engaged in the academic study of religion by shedding light on the porosity of boundaries that we moderns impose on the past to fit modern agendas.
University Museums
Authors: Simpson Andrew
Published: June 2024

There has long been a close relationship between the process of collection building and their use in the generation and transmission of knowledge. However, it has only been in recent decades that university museums have been considered an identifiable field of inquiry, mainly as a specialism of museology that results from the close alignment of material collections in the higher education academy. Much of the writing about the history of museology has either played down or overlooked the relationship with organizational structures dedicated to higher learning. The archetype of what is widely considered to be the modern university museum is the Ashmolean Museum at Oxford University. The development of the modern museum and the modern university stem from the 17th century when the religious focus of culture and intellectual life of the Middle Ages was supplanted by a wave of curiosity and experimentation that fractured the old knowledge systems of natural philosophy into a range of distinctive new scientific disciplines. Associated with this timing was the expansion of European empires and collecting natural and cultural objects, including human remains, from the New World on a massive scale and bringing them back to the center of empires for the new knowledge-building academic enterprises. This accumulation of materiality served a new era of knowledge generation based on classification in firstly Linnaean, then Darwinian, traditions. The same classificatory approach was replicated in cultural investigations of different peoples that established frameworks for knowledge systems in humanistic disciplines as well as scientific ones. Much of the early writing about university museums has captured disciplinary histories rather than articulated a theoretical basis for the close alignment between knowledge and materiality. Part of the reason for this is that the museum and the university, at least in their modern and most familiar form, have been considered two completely different types of organization.
Third Battle of Panipat
Authors: Roy Kaushik
Published: June 2024

The Third Battle of Panipat fought on 14 January 1761 was one of the decisive battles of the early modern era. However, people outside India do not know much about this gigantic clash between the Marathas and the Afghans. Some forty-five thousand Maratha troops under Sadashiv Rao Bhau fought against sixty-two thousand soldiers (Afghans and their Indian allies) under the leadership of Ahmad Shah Abdali at Panipat, some one hundred kilometers north of Delhi. This battlefield had witnessed two battles earlier (known as the First and Second Battles of Panipat fought on 20 April 1526 and 5 November 1556 respectively) between the Mughals and the Afghans. In both cases the Mughals emerged victorious. The day-long Third Battle of Panipat resulted in twenty thousand casualties on the Maratha side. After the battle, some forty thousand non-combatants from the Maratha camp were captured. About half of them (mostly females) were sold as slaves and the rest were executed. This battle changed the course of South Asian history in particular and global history in general. The Marathas were down and out and the Afghan Durrani Empire was too exhausted to reap the fruits of victory. This left the field open for the British East India Company to expand its sway over the Indian subcontinent in the second half of the 18th century. The establishment of the British Empire in India in turn significantly influenced the course of world history. Historians even now debate about the course and consequences of Panipat. Different communities memorized warfare in the 18th century and continue to do so. This essay takes into account the debates concerning the causes, course, and consequences of the battle. Both structural factors and human agency played a role in this story. The Mughal economy was slowing down due to long-term impersonal factors. Factional fighting among inefficient Mughal nobles also accelerated the collapse of the Mughal imperium. The different regional factors that influenced Afghan and Maratha policies are analyzed. For instance, the decay of Mughal power in central and north India allowed the Marathas to invade Punjab. The rapid Mughal collapse in Punjab enabled Abdali to intervene in India. In addition to the military aspects, the social, economic, and cultural dimensions of this climactic conflict have been considered. Academic studies of early modern Afghanistan are few compared to those of India. Hence, it is difficult to provide a balanced story. Finally, an attempt is made to put this battle in the global context.