bluuebunny/crossref_metadata_2025_split huggingface dataset:
HFCF‐Net: A hybrid‐feature cross fusion network for COVID‐19 lesion segmentation from CT volumetric images
Authors: Wang Yanting , Yang Qingyu , Tian Lixia , Zhou Xuezhong , Rekik Islem , Huang Huifang 
Published: March 2022

AbstractBackgroundThe coronavirus disease 2019 (COVID‐19) spreads rapidly across the globe, seriously threatening the health of people all over the world. To reduce the diagnostic pressure of front‐line doctors, an accurate and automatic lesion segmentation method is highly desirable in clinic practice.PurposeMany proposed two‐dimensional (2D) methods for sliced‐based lesion segmentation cannot take full advantage of spatial information in the three‐dimensional (3D) volume data, resulting in limited segmentation performance. Three‐dimensional methods can utilize the spatial information but suffer from long training time and slow convergence speed. To solve these problems, we propose an end‐to‐end hybrid‐feature cross fusion network (HFCF‐Net) to fuse the 2D and 3D features at three scales for the accurate segmentation of COVID‐19 lesions.MethodsThe proposed HFCF‐Net incorporates 2D and 3D subnets to extract features within and between slices effectively. Then the cross fusion module is designed to bridge 2D and 3D decoders at the same scale to fuse both types of features. The module consists of three cross fusion blocks, each of which contains a prior fusion path and a context fusion path to jointly learn better lesion representations. The former aims to explicitly provide the 3D subnet with lesion‐related prior knowledge, and the latter utilizes the 3D context information as the attention guidance of the 2D subnet, which promotes the precise segmentation of the lesion regions. Furthermore, we explore an imbalance‐robust adaptive learning loss function that includes image‐level loss and pixel‐level loss to tackle the problems caused by the apparent imbalance between the proportions of the lesion and non‐lesion voxels, providing a learning strategy to dynamically adjust the learning focus between 2D and 3D branches during the training process for effective supervision.ResultExtensive experiments conducted on a publicly available dataset demonstrate that the proposed segmentation network significantly outperforms some state‐of‐the‐art methods for the COVID‐19 lesion segmentation, yielding a Dice similarity coefficient of 74.85%. The visual comparison of segmentation performance also proves the superiority of the proposed network in segmenting different‐sized lesions.ConclusionsIn this paper, we propose a novel HFCF‐Net for rapid and accurate COVID‐19 lesion segmentation from chest computed tomography volume data. It innovatively fuses hybrid features in a cross manner for lesion segmentation, aiming to utilize the advantages of 2D and 3D subnets to complement each other for enhancing the segmentation performance. Benefitting from the cross fusion mechanism, the proposed HFCF‐Net can segment the lesions more accurately with the knowledge acquired from both subnets.
Voxel‐wise supervised analysis of tumors with multimodal engineered features to highlight interpretable biological patterns
Authors: Escobar Thibault , Vauclin Sébastien , Orlhac Fanny , Nioche Christophe , Pineau Pascal , Champion Laurence , Brisse Hervé , Buvat Irène 
Published: March 2022

AbstractBackgroundTranslation of predictive and prognostic image‐based learning models to clinical applications is challenging due in part to their lack of interpretability. Some deep‐learning‐based methods provide information about the regions driving the model output. Yet, due to the high‐level abstraction of deep features, these methods do not completely solve the interpretation challenge. In addition, low sample size cohorts can lead to instabilities and suboptimal convergence for models involving a large number of parameters such as convolutional neural networks.PurposeHere, we propose a method for designing radiomic models that combines the interpretability of handcrafted radiomics with a sub‐regional analysis.Materials and methodsOur approach relies on voxel‐wise engineered radiomic features with average global aggregation and logistic regression. The method is illustrated using a small dataset of 51 soft tissue sarcoma (STS) patients where the task is to predict the risk of lung metastasis occurrence during the follow‐up period.ResultsUsing positron emission tomography/computed tomography and two magnetic resonance imaging sequences separately to build two radiomic models, we show that our approach produces quantitative maps that highlight the signal that contributes to the decision within the tumor region of interest. In our STS example, the analysis of these maps identified two biological patterns that are consistent with STS grading systems and knowledge: necrosis development and glucose metabolism of the tumor.ConclusionsWe demonstrate how that method makes it possible to spatially and quantitatively interpret radiomic models amenable to sub‐regions identification and biological interpretation for patient stratification.
Ultra‐high‐resolution depth‐encoding small animal PET detectors: Using GAGG and LYSO crystal arrays
Authors: Niu Ming , Liu Zheng , Kuang Zhonghua , Wang Xiaohui , Ren Ning , Sang Ziru , Wu San , Cong Longhan , Sun Tao , Hu Zhanli , Yang Yongfeng 
Published: March 2022

AbstractPurposeSmall animal positron emission tomography (PET) scanners are widely used in current biomedical research. The study aimed to develop high‐efficiency and ultra‐high‐resolution detectors that could be used to develop a small animal PET scanner with high sensitivity and spatial resolution approaching to its physical limit.MethodsFour crystal arrays were fabricated and measured in this study. Crystal arrays 1 and 2 consisted of 38 × 38 gadolinium aluminum gallium garnet (GAGG) and lutetium–yttrium oxyorthosilicate (LYSO) crystals of 0.4 × 0.4 × 20 mm3 size. Crystal array 3 consisted of 16 × 16 GAGG crystals of 0.3 × 0.3 × 20 mm3 size, and crystal array 4 consisted of 24 × 24 LYSO crystals 0.3 × 0.3 × 20 mm3 in size. The crystal arrays were dual‐ended readouts using 8 × 8 silicon photomultiplier (SiPM) arrays of 2 × 2 mm2 pixel area. The SiPM array was readout using a signal multiplexing circuit to convert the 64 output signals into four position‐encoding signals. The performances of the four detectors in terms of flood histogram, energy resolution, depth of interaction (DOI) resolution, and timing resolution were measured.ResultsThe GAGG detectors provided better flood histograms, ∼30% higher photopeak amplitude, ∼20% higher energy resolution, ∼12% worse DOI resolution, and ∼15% worse timing resolution compared with LYSO detectors of the same crystal size. These four detectors provided DOI resolutions of <2 mm, energy resolutions of <22%, and timing resolutions of <1.6 ns. All crystals of 0.4 × 0.4 × 20 mm3 and 0.3 × 0.3 × 20 mm3 could be clearly resolved if the crystal array was 1 mm smaller in the four sides than that in the SiPM array.ConclusionsHigh DOI resolution PET detectors were developed using both GAGG and LYSO arrays with crystal sizes of 0.3 and 0.4 mm, respectively, and a length of 20 mm. The detectors can be used in the future to develop small animal PET scanners, especially dedicated mouse imaging PET scanners, which can simultaneously achieve high sensitivity and ultra‐high spatial resolution.
In high‐grade ovarian carcinoma, platinum‐sensitive tumor recurrence and acquired‐resistance derive from quiescent residual cancer cells that overexpress CRYAB, CEACAM6, and SOX2
Authors: du Manoir Stanislas , Delpech Hélène , Orsetti Béatrice , Jacot William , Pirot Nelly , Noel Jean , Colombo Pierre‐Emmanuel , Sardet Claude , Theillet Charles 
Published: March 2022

AbstractMost high‐grade ovarian carcinomas (HGOCs) are sensitive to carboplatin (CBP)‐based chemotherapy but frequently recur within 24 months. Recurrent tumors remain CBP‐sensitive and acquire resistance only after several treatment rounds. Recurrences arise from a small number of residual tumor cells not amenable to investigation in patients. We developed patient‐derived xenografts (PDXs) that allow the study of these different stages of CBP‐sensitive recurrence and acquisition of resistance. We generated PDX models from CBP‐sensitive and intrinsically resistant HGOC. PDXs were CBP‐ or mock‐treated and tumors were sampled, after treatment and at recurrence. We also isolated models with acquired‐resistance from CBP‐sensitive PDXs. Tumors were characterized at the histological and transcriptome levels. PDX models reproduced treatment response seen in the patients. CBP‐sensitive residual tumors contained nonproliferating tumor cell clusters embedded in a fibrotic mesh. In nontreated PDX tumors and treated CBP‐resistant tumors, fibrotic tissue was not prevalent. Residual tumors had marked differences in gene expression when compared to naïve and recurrent tumors, indicating downregulation of the cell cycle and proliferation and upregulation of interferon response and the epithelial–mesenchymal transition. This gene expression pattern resembled that described in embryonal diapause and ‘drug‐tolerant persister’ states. Residual and acquired‐resistance tumors share the overexpression of three genes: CEACAM6, CRYAB, and SOX2. Immunostaining analysis showed strong CEACAM6, CRYAB, and SOX2 protein expression in CBP‐sensitive residual and acquired‐resistance PDX, thus confirming the RNA profiling results. In HGOC PDX, CBP‐sensitive recurrences arise from a small population of quiescent, drug‐tolerant, residual cells embedded in a fibrotic mesh. These cells overexpress CEACAM6, CRYAB, and SOX2, whose overexpression is also associated with acquired resistance and poor patient prognosis. CEACAM6, CRYAB, and SOX2 may thus serve as a biomarker to predict recurrence and emergence of resistant disease in CBP‐treated HGOC patients. © 2022 The Pathological Society of Great Britain and Ireland.
Supporting practitioners in school‐based evaluations of autism spectrum disorders
Authors: Harry Sarah W. , Bates‐Brantley Kayla E. , Whitefield Breya L. , Dale Brittany A. 
Published: March 2022

AbstractStudents with autism spectrum disorder (ASD) have vastly different educational needs. Although some students with ASD may perform well across subjects within the general education classroom, other students with ASD may need more individualized support outside of the classroom. Historically, ASD assessments in schools have primarily focused on the measurement of cornerstone behaviors of ASD such as deficits in social communication and restricted or repetitive behaviors while underestimating the focus of academic skills even though both factors are required in the evaluation process and for an eligibility classification. The purpose of this article is to provide an overview of academic assessment practices in the schools by highlighting best practices in ASD evaluation, outlining ASD academic profiles and how to identify academic skill deficits, and reviewing the available literature that comes from different formal‐ and function‐based assessment practices that are commonly used in schools today. The authors also discuss how formal‐ and function‐based assessments both serve a purpose and are recommended to be used in conjunction with one another to best demonstrate a student's academic profile. Practitioners are ultimately encouraged to use a multi‐informant, multi‐modal approach when it comes to psychoeducational evaluations for individuals with ASD as it is evident that an individualized approach is essential due to the discrepancy of academic profiles related to this disability category as well as understanding that no measure is a perfect representation of any one skill.
Evaluation of cardiac parameters and other safety outcomes of brolucizumab treatment in patients with neovascular age‐related macular degeneration
Authors: Zakaria Nadia , Guerard Nicolas , Emanuelli Andres , Dugel Pravin , Watts Jen , Liew Melissa , Gekkieva Margarita , Hinder Markus 
Published: March 2022

AbstractThis was a prospective, single‐dose, single‐arm, open‐label, non‐randomized, multicenter clinical study to determine cardiovascular safety after a single brolucizumab 6 mg intravitreal injection in neovascular age‐related macular degeneration patients (N = 14). Electrocardiogram (ECG) data were collected at different time points using 12‐lead Holter and standard ECG, and patients were followed up to 8 days (end of study) for any signs of ocular and non‐ocular adverse events (AEs). No clinically meaningful changes were observed in cardiac parameters. No patient had a ≥30 msec change from baseline in heart rate–corrected QT using Fridericia's formula (QTcF), and no patient had a new QTcF value of ≥450 msec between 20 and 24 h after treatment. No deaths or serious AEs were reported during the study period. These results are in line with the absence of new cardiovascular safety signal based on the ECG recordings collected over the first year of the pivotal studies performed with brolucizumab in DME.Trial Registration: ClinicalTrials.gov identifier: NCT03954626.
Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing
Authors: Rosignoli Serena , Cosenza Francesco , Moscou Matthew J. , Civolani Laura , Musiani Francesco , Forestan Cristian , Milner Sara Giulia , Savojardo Castrense , Tuberosa Roberto , Salvi Silvio 
Published: March 2022

AbstractDisease lesion mimic (DLM) or necrotic mutants display necrotic lesions in the absence of pathogen infections. They can show improved resistance to some pathogens and their molecular dissection can contribute to revealing components of plant defense pathways. Although forward‐genetics strategies to find genes causal to mutant phenotypes are available in crops, these strategies require the production of experimental cross populations, mutagenesis, or gene editing and are time‐ and resource‐consuming or may have to deal with regulated plant materials. In this study, we described a collection of 34 DLM mutants in barley (Hordeum vulgare L.) and applied a novel method called complementation by sequencing (CBS), which enables the identification of the gene responsible for a mutant phenotype given the availability of two or more chemically mutagenized individuals showing the same phenotype. Complementation by sequencing relies on the feasibility to obtain all induced mutations present in chemical mutants and on the low probability that different individuals share the same mutated genes. By CBS, we identified a cytochrome P450 CYP71P1 gene as responsible for orange blotch DLM mutants, including the historical barley nec3 locus. By comparative phylogenetic analysis we showed that CYP71P1 gene family emerged early in angiosperm evolution but has been recurrently lost in some lineages including Arabidopsis thaliana (L.) Heynh. Complementation by sequencing is a straightforward cost‐effective approach to clone genes controlling phenotypes in a chemically mutagenized collection. The TILLMore (TM) collection will be instrumental for understanding the molecular basis of DLM phenotypes and to contribute knowledge about mechanisms of host–pathogen interaction.
Nonperturbative negative geometries: amplitudes at strong coupling and the amplituhedron
Authors: Arkani-Hamed Nima , Henn Johannes , Trnka Jaroslav 
Published: March 2022

Abstract
The amplituhedron determines scattering amplitudes in planar $$ \mathcal{N} $$
N
= 4 super Yang-Mills by a single “positive geometry” in the space of kinematic and loop variables. We study a closely related definition of the amplituhedron for the simplest case of four-particle scattering, given as a sum over complementary “negative geometries”, which provides a natural geometric understanding of the exponentiation of infrared (IR) divergences, as well as a new geometric definition of an IR finite observable $$ \mathcal{F} $$
F
(g, z) — dually interpreted as the expectation value of the null polygonal Wilson loop with a single Lagrangian insertion — which is directly determined by these negative geometries. This provides a long-sought direct link between canonical forms for positive (negative) geometries, and a completely IR finite post-loop-integration observable depending on a single kinematical variable z, from which the cusp anomalous dimension Γcusp(g) can also be straightforwardly obtained. We study an especially simple class of negative geometries at all loop orders, associated with a “tree” structure in the negativity conditions, for which the contributions to $$ \mathcal{F} $$
F
(g, z) and Γcusp can easily be determined by an interesting non-linear differential equation immediately following from the combinatorics of negative geometries. This lets us compute these “tree” contributions to $$ \mathcal{F} $$
F
(g, z) and Γcusp for all values of the ‘t Hooft coupling. The result for Γcusp remarkably shares all main qualitative characteristics of the known exact results obtained using integrability.
BTK inhibition limits B-cell–T-cell interaction through modulation of B-cell metabolism: implications for multiple sclerosis therapy
Authors: Li Rui , Tang Hao , Burns Jeremy C. , Hopkins Brian T. , Le Coz Carole , Zhang Bo , de Barcelos Isabella Peixoto , Romberg Neil , Goldstein Amy C. , Banwell Brenda L. , Luning Prak Eline T. , Mingueneau Michael , Bar-Or Amit 
Published: March 2022

AbstractInhibition of Bruton’s Tyrosine Kinase (BTKi) is now viewed as a promising next-generation B-cell-targeting therapy for autoimmune diseases including multiple sclerosis (MS). Surprisingly little is known; however, about how BTKi influences MS disease-implicated functions of B cells. Here, we demonstrate that in addition to its expected impact on B-cell activation, BTKi attenuates B-cell:T-cell interactions via a novel mechanism involving modulation of B-cell metabolic pathways which, in turn, mediates an anti-inflammatory modulation of the B cells. In vitro, BTKi, as well as direct inhibition of B-cell mitochondrial respiration (but not glycolysis), limit the B-cell capacity to serve as APC to T cells. The role of metabolism in the regulation of human B-cell responses is confirmed when examining B cells of rare patients with mitochondrial respiratory chain mutations. We further demonstrate that both BTKi and metabolic modulation ex vivo can abrogate the aberrant activation and costimulatory molecule expression of B cells of untreated MS patients. Finally, as proof-of-principle in a Phase 1 study of healthy volunteers, we confirm that in vivo BTKi treatment reduces circulating B-cell mitochondrial respiration, diminishes their activation-induced expression of costimulatory molecules, and mediates an anti-inflammatory shift in the B-cell responses which is associated with an attenuation of T-cell pro-inflammatory responses. These data collectively elucidate a novel non-depleting mechanism by which BTKi mediates its effects on disease-implicated B-cell responses and reveals that modulating B-cell metabolism may be a viable therapeutic approach to target pro-inflammatory B cells.
Hypothermic circulatory arrest does not induce coagulopathy in vitro
Authors: Ise Hayato , Oyama Kyohei , Kunioka Shingo , Shirasaka Tomonori , Kanda Hirotsugu , Akhyari Payam , Kamiya Hiroyuki 
Published: March 2022

AbstractHypothermic circulatory arrest (HCA) is an essential procedure during aortic surgery to protect organs; however, hypothermia is believed to cause coagulopathy, which is a major fatal complication. This study aimed to clarify the impact of hypothermia on coagulation by eliminating clinical biases in vitro. In the hypothermic storage study, blood samples from five healthy volunteers were stored at 37 ℃ (group N) for 3 h or at 20 ℃ for 2 h, followed by 1 h of rewarming at 37 ℃ (group H). Thromboelastography was performed before and after 3 h of storage. In the mock circulation loop (MCL) study, blood samples were placed in the MCL and (a) maintained at 37 ℃ for 4 h (group N, n = 5), or (b) cooled to 20 ℃ to simulate HCA with a 0.1 L/min flow rate for 3 h and then rewarmed to 37 ℃ (group H, n = 5). The total MCL duration was 4 h, and the flow rate was maintained at 1 L/min, except during HCA. Blood samples collected 15 min after the beginning and end of MCL were subjected to standard laboratory tests and rotational thromboelastometry analyses. Hypothermia had no impact on coagulation in both the hypothermic storage and MCL studies. MCL significantly decreased the platelet counts and clot elasticity in the INTEM and EXTEM assays; however, there was no effect on fibrinogen contribution measured by FIBTEM. Hypothermia does not cause irreversible coagulopathy in vitro; however, MCL decreases coagulation due to the deterioration of platelets.
Quantifying the effects of environment and population diversity in multi-agent reinforcement learning
Authors: McKee Kevin R. , Leibo Joel Z. , Beattie Charlie , Everett Richard 
Published: March 2022

AbstractGeneralization is a major challenge for multi-agent reinforcement learning. How well does an agent perform when placed in novel environments and in interactions with new co-players? In this paper, we investigate and quantify the relationship between generalization and diversity in the multi-agent domain. Across the range of multi-agent environments considered here, procedurally generating training levels significantly improves agent performance on held-out levels. However, agent performance on the specific levels used in training sometimes declines as a result. To better understand the effects of co-player variation, our experiments introduce a new environment-agnostic measure of behavioral diversity. Results demonstrate that population size and intrinsic motivation are both effective methods of generating greater population diversity. In turn, training with a diverse set of co-players strengthens agent performance in some (but not all) cases.
Window dressing inequalities and constructing women farmers as problematic—gender in Rwanda’s agriculture policy
Authors: Andersson Karolin , Pettersson Katarina , Lodin Johanna Bergman 
Published: March 2022

AbstractRwanda is often depicted as a success story by policy makers when it comes to issues of gender. In this paper, we show how the problem of gendered inequality in agriculture nevertheless is both marginalized and instrumentalized in Rwanda’s agriculture policy. Our in-depth analysis of 12 national policies is informed by Bacchi’sWhat’s the problem represented to be?approach. It attests that gendered inequality is largely left unproblematized as well as reduced to a problem of women’s low agricultural productivity. The policy focuses on framing the symptoms and effects of gendered inequality and turns gender mainstreaming into an instrument for national economic growth. We argue that by insufficiently addressing the socio-political underlying causes of gendered inequality, Rwanda’s agriculture policy risks reproducing and exacerbating inequalities by reinforcing dominant gender relations and constructing women farmers as problematic and men as normative farmers. We call for the policy to approach gendered inequality in alternative ways. Drawing on perspectives in feminist political ecology, we discuss how such alternatives could allow policy to more profoundly challenge underlying structural constraints such as unequal gender relations of power, gender norms, and gender divisions of work. This would shift policy’s problematizing lens from economic growth to social justice, and from women’s shortcomings and disadvantages in agriculture to the practices and relations that perpetuate inequality. In the long term, this could lead to transformed gender norms and power relations, and a more just and equal future beyond what the dominant agricultural development discourse currently permits.