bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of D3-type cyclins is related to cytokinin and the bHLH transcription factor SPATULA in Arabidopsis gynoecium development
Authors: Cerbantez-Bueno Vincent E. , Serwatowska Joanna , Rodríguez-Ramos Carolina , Cruz-Valderrama J. Erik , de Folter Stefan 
Published: July 2024

Abstract
Main conclusion
We studied the D3-type cyclin function during gynoecium development in Arabidopsis and how they are related to the hormone cytokinin and the transcription factor SPATULA.

Abstract
Growth throughout the life of plants is sustained by cell division and differentiation processes in meristematic tissues. In Arabidopsis, gynoecium development implies a multiphasic process where the tissues required for pollination, fertilization, and seed development form. The Carpel Margin Meristem (CMM) is a mass of undifferentiated cells that gives rise to the gynoecium internal tissues, such as septum, ovules, placenta, funiculus, transmitting tract, style, and stigma. Different genetic and hormonal factors, including cytokinin, control the CMM function. Cytokinin regulates the cell cycle transitions through the activation of cell cycle regulators as cyclin genes. D3-type cyclins are expressed in proliferative tissues, favoring the mitotic cell cycle over the endoreduplication. Though the role of cytokinin in CMM and gynoecium development is highly studied, its specific role in regulating the cell cycle in this tissue remains unclear. Additionally, despite extensive research on the relationship between CYCD3 genes and cytokinin, the regulatory mechanism that connects them remains elusive. Here, we found that D3-type cyclins are expressed in proliferative medial and lateral tissues. Conversely, the depletion of the three CYCD3 genes showed that they are not essential for gynoecium development. However, the addition of exogenous cytokinin showed that they could control the division/differentiation balance in gynoecium internal tissues and outgrowths. Finally, we found that SPATULA can be a mechanistic link between cytokinin and the D3-type cyclins. The data suggest that the role of D3-type cyclins in gynoecium development is related to the cytokinin response, and they might be activated by the transcription factor SPATULA.
Developing a deep learning model for predicting ovarian cancer in Ovarian-Adnexal Reporting and Data System Ultrasound (O-RADS US) Category 4 lesions: A multicenter study
Authors: Xie Wenting , Lin Wenjie , Li Ping , Lai Hongwei , Wang Zhilan , Liu Peizhong , Huang Yijun , Liu Yao , Tang Lina , Lyu Guorong 
Published: July 2024

Abstract
Purpose
To develop a deep learning (DL) model for differentiating between benign and malignant ovarian tumors of Ovarian-Adnexal Reporting and Data System Ultrasound (O-RADS US) Category 4 lesions, and validate its diagnostic performance.

Methods
A retrospective analysis of 1619 US images obtained from three centers from December 2014 to March 2023. DeepLabV3 and YOLOv8 were jointly used to segment, classify, and detect ovarian tumors. Precision and recall and area under the receiver operating characteristic curve (AUC) were employed to assess the model performance.

Results
A total of 519 patients (including 269 benign and 250 malignant masses) were enrolled in the study. The number of women included in the training, validation, and test cohorts was 426, 46, and 47, respectively. The detection models exhibited an average precision of 98.68% (95% CI: 0.95–0.99) for benign masses and 96.23% (95% CI: 0.92–0.98) for malignant masses. Moreover, in the training set, the AUC was 0.96 (95% CI: 0.94–0.97), whereas in the validation set, the AUC was 0.93(95% CI: 0.89–0.94) and 0.95 (95% CI: 0.91–0.96) in the test set. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive values for the training set were 0.943,0.957,0.951,0.966, and 0.936, respectively, whereas those for the validation set were 0.905,0.935, 0.935,0.919, and 0.931, respectively. In addition, the sensitivity, specificity, accuracy, positive predictive value, and negative predictive value for the test set were 0.925, 0.955, 0.941, 0.956, and 0.927, respectively.

Conclusion
The constructed DL model exhibited high diagnostic performance in distinguishing benign and malignant ovarian tumors in O-RADS US category 4 lesions.
Cortical Activation during Swallowing Exercise Tasks: an fNIRS Pilot Study
Authors: Chua Denise Mae N. , Chan Karen Man-Kei 
Published: July 2024

AbstractThis pilot study used functional near-infrared spectroscopy (fNIRS) to examine brain activity in selected regions of the left motor and sensory cortex while doing swallowing-related tasks. Specifically, differences in cortical activation during normal saliva swallows, effortful swallows, and tongue pressing were investigated. Nine healthy, right-handed adults (5 female, 4 male; Age: 22–30 years) were recruited. The tasks included were (1) normal saliva swallowing, (2) effortful saliva swallowing, and (3) lingual pressing against the palate. Each task was completed three times in a block, for a total of five blocks. Blocks were randomized and presented with set time intervals using PsychoPy. Motor activity was highest during effortful swallows, followed by normal swallows, and lingual presses. Activation in the sensory region was not significantly different across tasks; however, effortful swallows elicited the highest mean peak activation. Our findings suggest that fNIRS can be a viable imaging method used to examine differences in cortical activity in the context of swallowing. Its applicability in future dysphagia research should be explored.
Subtotal laparoscopic cholecystectomy versus conversion to open as a bailout procedure: a cohort study
Authors: Ramírez-Giraldo Camilo , Monroy Danny Conde , Isaza-Restrepo Andrés , Ayala Daniela , González-Tamayo Juliana , Vargas-Patiño Ana Maria , Trujillo-Guerrero Luisa , Van-Londoño Isabella , Rojas-López Susana 
Published: July 2024

Abstract
Background
The aim of this study is to evaluate morbidity and mortality in patients taken to conversion to open procedure (CO) and subtotal laparoscopic cholecystectomy (SLC) as bailout procedures when performing difficult laparoscopic cholecystectomy.

Method
This observational cohort study retrospectively analyzed patients taken to SLC or CO as bailout surgery during difficult laparoscopic cholecystectomy between 2014 and 2022. Univariable and multivariable logistic regression models were used to identify prognostic factors for morbimortality.

Results
A total of 675 patients were included. Of the 675 patients (mean [SD] age 63.85 ± 16.00 years; 390 [57.7%] male) included in the analysis, 452 (67%) underwent CO and 223 (33%) underwent SLC. Overall, neither procedure had an increased risk of major complications (89 [19.69%] vs 35 [15.69%] P.207). However, CO had an increased risk of bile duct injury (18 [3.98] vs 1 [0.44] P.009), bleeding (mean [SD] 165.43 ± 368.57 vs 43.25 ± 123.42 P < .001), intestinal injury (20 [4.42%] vs 0 [0.00] P.001), and wound infection (18 [3.98%] vs 2 [0.89%] P.026), while SLC had a higher risk of bile leak (15 [3.31] vs 16 [7.17] P.024). On the multivariable analysis, Charlson comorbidity index (odds ratio [OR], 1.20; CI95%, 1.01–1.42), use of anticoagulant agents (OR, 2.56; CI95%, 1.21–5.44), classification of severity of cholecystitis grade III (OR, 2.96; CI95%, 1.48–5.94), and emergency admission (OR, 6.07; CI95%, 1.33–27.74) were associated with presenting major complications.

Conclusions
SLC was less associated with complications; however, there is scant evidence on its long-term outcomes. Further research is needed on SLC to establish if it is the safest in the long-term as a bailout procedure.
Spontaneous emergence of deformation bands in single-crystal plasticity simulations at small strain
Authors: Ryś M. , Kursa M. , Petryk H. 
Published: July 2024

Abstract
In metal single crystals, the observed formation of deformation banding pattern has been explained by greater latent hardening of slip systems than their self-hardening, which promotes spatial segregation of plastic slips and lamination towards single-slip domains. Numerical studies focusing on the formation of deformation bands usually involved initial imperfections, boundary-induced heterogeneity, or the postulate of minimal global energy expenditure which additionally promoted non-uniformity of deformation. This article analyses the case when no such mechanism enforcing locally non-uniform deformation is implemented in the finite element (FE) method, while the global system of equations of incremental equilibrium is solved in a standard way. The new finding in this paper is that the deformation banding pattern can appear spontaneously in FE simulations of homogeneous single crystals even in the absence of any mechanism favouring deformation banding in the numerical code. This has been demonstrated in several examples in the small strain formalism using a plane-strain model in which the twelve fcc slip systems are reduced to three effective plastic slip mechanisms. Incremental slips are determined at the Gauss-point level either by incremental work minimization in the rate-independent case or by rate-dependent regularization. In the rate-independent approach, the trust-region algorithm is developed for the selection of active slip systems with the help of the augmented Lagrangian method. Conditions under which a banding pattern appears spontaneously or is suppressed are discussed. In particular, a critical rate sensitivity exponent is identified.
Immunity in digestive diseases: new drugs for inflammatory bowel disease treatment—insights from Phase II and III trials
Authors: Massironi Sara , Furfaro Federica , Bencardino Sarah , Allocca Mariangela , Danese Silvio 
Published: July 2024

Abstract
Background
Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), continues to challenge treatment paradigms. Advancements in therapeutic options have been have been driven by Phase 2 and 3 clinical trials of new drug classes, particularly sphingosine-1-phosphate (S1P) modulators and interleukin-23 (IL-23) inhibitors.

Methods
This review synthesizes findings from Phase 2 and 3 clinical trials conducted up to early 2024, focusing on the impact of S1P modulators and IL-23 inhibitors on IBD management. Drugs such as ozanimod, etrasimod, risankizumab, mirikizumab, guselkumab, and brasikumab were evaluated for their efficacy and safety profiles.

Results
S1P modulators, such as ozanimod and etrasimod, effectively regulate immune cell trafficking to reduce inflammation and several trials highlight their clinical effectiveness in both inducing and maintaining remission in IBD, highlighting its long-term safety and sustained therapeutic effects. Additionally, IL-23 inhibitors including risankizumab, mirikizumab, and guselkumab, which disrupt key inflammatory cytokine pathways, have already shown significant effectiveness in inducing and maintaining remission in both CD and UC, with favorable safety profiles across multiple studies, suggesting their potential as critical components in managing IBD.

Conclusions
The clinical trials indicate that both S1P modulators and IL-23 inhibitors offer promising therapeutic benefits and maintain strong safety profiles, positioning them as potential cornerstone treatments for IBD. Despite these advancements, further exploration into long-term safety and the development of personalized treatment strategies is essential for maximizing clinical outcomes.
A new colorimetric lactate biosensor based on CUPRAC reagent using binary enzyme (lactate-pyruvate oxidases)-immobilized silanized magnetite nanoparticles
Authors: Ayaz Selen , Erşan Teslime , Dilgin Yusuf , Apak Reşat 
Published: July 2024

Abstract A novel optical lactate biosensor is presented that utilizes a colorimetric interaction between H2O2 liberated by a binary enzymatic reaction and bis(neocuproine)copper(II) complex ([Cu(Nc)2]2+) known as CUPRAC (cupric reducing antioxidant capacity) reagent. In the first step, lactate oxidase (LOx) and pyruvate oxidase (POx) were separately immobilized on silanized magnetite nanoparticles (SiO2@Fe3O4 NPs), and thus, 2 mol of H2O2 was released per 1 mol of the substrate due to a sequential enzymatic reaction of the mixture of LOx-SiO2@Fe3O4 and POx-SiO2@Fe3O4 NPs with lactate and pyruvate, respectively. In the second step, the absorbance at 450 nm of the yellow-orange [Cu(Nc)2]+ complex formed through the color reaction of enzymatically produced H2O2 with [Cu(Nc)2]2+ was recorded. The results indicate that the developed colorimetric binary enzymatic biosensor exhibits a broad linear range of response between 0.5 and 50.0 µM for lactate under optimal conditions with a detection limit of 0.17 µM. The fabricated biosensor did not respond to other saccharides, while the positive interferences of certain reducing compounds such as dopamine, ascorbic acid, and uric acid were minimized through their oxidative removal with a pre-oxidant (NaBiO3) before enzymatic and colorimetric reactions. The fabricated optical biosensor was applied to various samples such as artificial blood, artificial/real sweat, and cow milk. The high recovery values (close to 100%) achieved for lactate-spiked samples indicate an acceptable accuracy of this colorimetric biosensor in the determination of lactate in real samples. Due to the increase in H2O2 production with the bienzymatic lactate sensor, the proposed method displays double-fold sensitivity relative to monoenzymatic biosensors and involves a neat color reaction with cupric-neocuproine having a clear stoichiometry as opposed to the rather indefinite stoichiometry of analogous redox dye methods.
Graphical Abstract
Use of intensive care, intracranial pressure monitoring, and external ventricular drainage devises in patients with bacterial meningitis, a cohort study
Authors: Tetens Malte M. , Roed Casper , Bodilsen Jacob , Omland Lars H. , Mens Helene , Lebech Anne-Mette , Obel Niels , Møller Kirsten , Rasmussen Rune , Overgaard-Steensen Christian , Perner Anders , Ziebell Morten , Andersen Åse B. 
Published: July 2024

Abstract

Background
Bacterial meningitis can cause a life-threatening increase in intracranial pressure (ICP). ICP-targeted treatment including an ICP monitoring device and external ventricular drainage (EVD) may improve outcomes but is also associated with the risk of complications. The frequency of use and complications related to ICP monitoring devices and EVDs among patients with bacterial meningitis remain unknown. We aimed to investigate the use of ICP monitoring devices and EVDs in patients with bacterial meningitis including frequency of increased ICP, drainage of cerebrospinal fluid (CSF), and complications associated with the insertion of ICP monitoring and external ventricular drain (EVD) in patients with bacterial meningitis.

Method
In a single-center prospective cohort study (2017–2021), we examined the frequency of use and complications of ICP-monitoring devices and EVDs in adult patients with bacterial meningitis.

Results
We identified 108 patients with bacterial meningitis admitted during the study period. Of these, 60 were admitted to the intensive care unit (ICU), and 47 received an intracranial device (only ICP monitoring device N = 16; EVD N = 31). An ICP > 20 mmHg was observed in 8 patients at insertion, and in 21 patients (44%) at any time in the ICU. Cerebrospinal fluid (CSF) was drained in 24 cases (51%). Severe complications (intracranial hemorrhage) related to the device occurred in two patients, but one had a relative contraindication to receiving a device.

Conclusions
Approximately half of the patients with bacterial meningitis needed intensive care and 47 had an intracranial device inserted. While some had conservatively correctable ICP, the majority needed CSF drainage. However, two patients experienced serious adverse events related to the device, potentially contributing to death. Our study highlights that the incremental value of ICP measurement and EVD in managing of bacterial meningitis requires further research.
Endpoint estimates for riesz transform on manifolds with ends
Authors: He Dangyang 
Published: July 2024

Abstract
We consider a class of non-doubling manifolds

$$\mathcal {M}$$

M

consisting of finite many “Euclidean” ends, where the Euclidean dimensions at infinity are not necessarily all the same. In [17], Hassell and Sikora proved that the Riesz transform on

$$\mathcal {M}$$

M

is of weak type (1, 1), bounded on

$$L^{p}$$

L
p

if and only if

$$1<p<n_*$$

1
<
p
<

n

∗

, where

$$n_* = \min _k n_k$$

n

∗

=

min
k

n
k

. In this note, we complete the picture by giving an endpoint estimate: Riesz transform is bounded on Lorentz space

$$L^{n_*,1}$$

L

n

∗

,
1

and unbounded from

$$L^{n_*,p}\rightarrow L^{n_*,q}$$

L

n

∗

,
p

→

L

n

∗

,
q

for all

$$1<p<\infty $$

1
<
p
<
∞

and

$$p\le q\le \infty $$

p
≤
q
≤
∞

.
Summary of the National Cancer Institute 2023 Virtual Workshop on Medical Image De-identification—Part 2: Pathology Whole Slide Image De-identification, De-facing, the Role of AI in Image De-identification, and the NCI MIDI Datasets and Pipeline
Authors: Clunie David , Taylor Adam , Bisson Tom , Gutman David , Xiao Ying , Schwarz Christopher G. , Greve Douglas , Gichoya Judy , Shih George , Kline Adrienne , Kopchick Ben , Farahani Keyvan 
Published: July 2024

Abstract
De-identification of medical images intended for research is a core requirement for data sharing initiatives, particularly as the demand for data for artificial intelligence (AI) applications grows. The Center for Biomedical Informatics and Information Technology (CBIIT) of the United States National Cancer Institute (NCI) convened a two half-day virtual workshop with the intent of summarizing the state of the art in de-identification technology and processes and exploring interesting aspects of the subject. This paper summarizes the highlights of the second day of the workshop, the recordings and presentations of which are publicly available for review. The topics covered included pathology whole slide image de-identification, de-facing, the role of AI in image de-identification, and the NCI Medical Image De-Identification Initiative (MIDI) datasets and pipeline.
Minimal Detectable Bone Fracture Gaps in CT Images and Digital Three-Dimensional (3D) Radii Models
Authors: Bittner-Frank Martin , Strassl Andreas , Unger Ewald , Hirtler Lena , Eckhart Barbara , Koenigshofer Markus , Stoegner Alexander , Staats Kevin , Kainberger Franz , Windhager Reinhard , Moscato Francesco , Benca Emir 
Published: July 2024

Abstract
Knowledge of the minimal detectable bone fracture gap is essential in three-dimensional (3D) models, particularly in pre-operative planning of osteosynthesis to avoid overlooking gaps. In this study, defined incisions and bony displacements ranging from 100 to 400 µm were created in diaphyseal radii in 20 paired forearm specimens and verified with light microscopy. The specimens were scanned utilizing different computed tomography (CT) technologies/scanners, specimen positionings, scan protocols, image segmentations, and processing protocols. Inter- and intra-operator variabilities were reported as coefficient kappa. In CT images, fracture gaps of 100 µm and bone lamellae of 300 µm and 400 µm width were identified at a rate of 80 to 100%, respectively, independent of the investigated settings. In contrast, only 400µm incisions and bony displacements were visible in digital 3D models, with detection rates dependent on CT technology, image segmentation, and post-processing algorithm. 3D bone models based on state-of-the-art CT imaging can reliably visualize clinically relevant bone fracture gap sizes. However, verification of fractures to be surgically addressed should be verified with the original CT image series.

Graphical Abstract
Free disposal hull models of multicomponent technologies
Authors: Papaioannou Grammatoula , Podinovski Victor V. 
Published: July 2024

AbstractFree disposal hull (FDH) is a nonparametric model of production technology based on the single assumption of free disposability of all inputs and outputs. In this paper, we consider multicomponent production technologies in which every decision making unit (DMU) consists of several parallel component processes that can in principle operate independently of each other, provided they have sufficient resources. An example is universities viewed as DMUs, with their departments or groups of departments viewed as component processes. Each component process uses its own set of inputs and an unknown part of the shared inputs in order to produce its own set of outputs and an unknown part of the shared outputs. We allow combinations of component processes taken from different DMUs in order to construct new hypothetical DMUs, and refer to the resulting model of technology as the multicomponent FDH (MFDH) model. We further develop a larger, and mathematically nontrivial, variant of MFDH for the case in which we can specify certain bounds on the proportions in which shared inputs and outputs are allocated to component processes. We use an illustrative example in the context of universities to demonstrate the increasing discriminatory power of the new MFDH models over the standard FDH models in the multicomponent setting.
Mental Health Evaluation of Younger and Older Adolescents Referred to the Center of Expertise on Gender Dysphoria in Amsterdam, The Netherlands
Authors: de Rooy Frédérique B. B. , Arnoldussen Marijn , van der Miesen Anna I. R. , Steensma Thomas D. , Kreukels Baudewijntje P. C. , Popma Arne , de Vries Annelou L. C. 
Published: July 2024

AbstractThe present study aimed to investigate whether differences exist between younger and older presenting adolescents at the Center of Expertise on Gender Dysphoria regarding psychological functioning and autistic traits. A total of 1487 consecutively assessed adolescents between 2000 and 2018 were divided in younger presenters (age ≤ 13.9 years) and older presenters (age ≥ 14 years). Of younger presenters, 227 (41.1%) were assigned male at birth and 325 (58.9%) assigned female at birth. In older presenters, 279 (29.8%) were assigned male at birth and 656 (70.2%) assigned female at birth. Behavioral and emotional problems were assessed with the Child Behavior Checklist (CBCL) and the Youth Self-Report (YSR). For autism traits, the Social Responsiveness Scale (SRS) was used. Compared to younger presenters, on both the CBCL and YSR older presenters had higher Total Problem (β = 1.75, p = .005, CI 0.53–2.97, R2 = .04 and β = 4.20, p < .001, CI 2.99–5.40, R2 = .07, respectively) and Internalizing Problem (β = 4.43, p < .001, CI 3.13–5.74, R2 = .06 and β = 6.69, p < .001, CI 5.31–8.07, R2 = .12, respectively) scores. Regarding autistic traits, a higher mean SRS total score was found in older presenting assigned males at birth (β = 4.55, p = .036, CI 0.30–8.81, R2 = .34). In assigned females at birth, no statistically significant difference between older and younger presenters was found in mean SRS total score (β = 1.19, p = .063, CI − 0.07 to 2.45, R2 = .39). Differences in mental health exist between younger and older presenting adolescents and call for an individualized approach in the clinical care of transgender adolescents.