bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary repair of nonsteroidal anti‐inflammatory drug‐associated full thickness gastrointestinal ulcers in 11 dogs
Authors: Dobberstein Rachel E. A. , Oblak Michelle L. , Brisson Brigitte A. , Singh Ameet , Moens Noel M. M. , Ayoub Sabrina 
Published: July 2022

AbstractObjectiveTo report the outcomes of dogs that underwent primary repair of gastroduodenal perforations associated with the administration of nonsteroidal anti‐inflammatory drugs (NSAID). A secondary objective was to identify clinicopathological findings that predisposed dogs to postoperative death.Study designRetrospective study.AnimalsEleven dogs with complete gastric or duodenal perforation related to administration of an NSAID that underwent primary surgical repair.MethodsMedical records were reviewed for dogs that presented with peritonitis due to a complete gastroduodenal perforation while receiving NSAIDs between November, 2011 and January, 2021. Data collected included patient characteristics, clinical signs, clinicopathological results, surgical details, and postoperative management and outcome.ResultsAll dogs were large breeds (mean weight 42 kg; range 22‐75 kg), with a mean age of 7.35 years. Nine dogs from a total of 11 (82 %) received a concurrent corticosteroid and NSAID, or a higher dose/frequency/length of NSAID administration than recommended by the manufacturer. All gastroduodenal perforations were found in the upper gastrointestinal tract. Eight of 11 (73%) dogs survived to discharge. The median postoperative duration of follow up was 444 days (range 2‐1460 days). No association was detected between ulcer size or location and mortality.ConclusionMost dogs who underwent primary repair of complete gastroduodenal ulcers survived. Gastroduodenal perforations were generally due to the administration of higher or longer doses of NSAIDs, or concurrent administration of another NSAID or corticosteroid.Clinical significancePrimary closure may be associated with a high success rate in dogs with full thickness gastroduodenal ulcers.
A Novel Screw Modeling Approach to Study the Effects of Screw Parameters on Pullout Strength
Authors: Song Fei , Feng Wentian , Yang Dongyue , Li Guanghui , Iqbal Kamran , Liu Yuxuan , Yang Haisheng 
Published: July 2022

Abstract
Screw loosening remains a prominent problem for osteoporotic patients undergoing pedicle screw fixation surgeries and is affected by screw parameters (e.g., diameter, pitch, and thread angle). However, the individual and interactive effects of these parameters on screw fixation are not fully understood. Furthermore, the current finite element modeling of a threaded screw is less computationally efficient. To address these issues, we (1) explored a novel “simulated threaded screw” approach (virtual threads assigned to the contact elements of a simplified screw) and compared its performance with threaded and simplified screws, and (2) examined this approach the individual and interactive effects of altering screw diameter (5.5–6.5 mm), pitch (1–2 mm) and half-thread angle (20–30 deg) on pullout strength of normal vertebrae. Results demonstrated that the “simulated threaded screw” approach equivalently predicted pullout strength compared to the “threaded screw” approach (R2 = 0.99, slope = 1). We further found that the pullout strength was most sensitive to the change in screw diameter, followed by thread angle, pitch, and interactions of diameter*pitch or diameter*angle. In conclusion, the “simulated threaded screw” approach can achieve the same predictive capability compared to threaded modeling of the screw. The current findings may serve as useful references for planning of screw parameters, so as to improve the complication of screw loosening.
Spontaneous large liver haematoma with extensive intraperitoneal bleeding in a patient with COVID-19 infection
Authors: Songtanin Busara , Evans Abbie , Nugent Kenneth 
Published: July 2022

Thrombotic complications during COVID-19 infections occur frequently, and anticoagulants to prevent and treat deep vein thrombosis appear to have a good safety profile in these patients. In addition, haemorrhagic complications during COVID-19 infections have also been reported. Hepatic inflammation can occur in COVID-19 infections as a direct consequence of cellular infection and cytopathy. Spontaneous subcapsular hepatic haematoma is extremely rare and can be life-threatening.A woman in her 40s presented to the hospital with fever and shortness of breath and was diagnosed with COVID-19 infection with respiratory failure requiring intubation. On day 49 of hospitalisation, she developed melena and acute anaemia; her haemoglobin dropped from 97g/L (9.7g/dL) to 56g/L (5.6g/dL). Abdominal and pelvic CT scans showed a large subcapsular liver haematoma with retroperitoneal extension. The patient received blood transfusions and remained haemodynamically stable. She was eventually extubated and discharged home.
Microbial determinants of effective donors in faecal microbiota transplantation for UC
Authors: Haifer Craig , Luu Laurence Don Wai , Paramsothy Sudarshan , Borody Thomas J , Leong Rupert W , Kaakoush Nadeem O 
Published: July 2022

ObjectiveFaecal microbiota transplantation (FMT) has variable efficacy in treating UC. Recently, oral lyophilised FMT was found to induce remission in patients with UC, with one donor having 100% efficacy compared with a second donor (36% efficacy). We characterised differences in the gut microbiota of these two donors with the aim of improving FMT donor selection.DesignFaecal samples from the two donors were collected over a period of 44 (donor 1) or 70 (donor 2) weeks. The microbiome and metabolome were profiled using shotgun metagenomics and untargeted metabolomicsResultsGut microbiome long-term stability was highly evident in the effective donor. Donor microbiota species evenness was a robust feature associated with clinical efficacy across two clinical trials of FMT in UC, leading to increased donor species engraftment in patients. Alpha diversity and beta diversity of donor gut microbiotas significantly differed. 90 bacterial species and one archaeon were differentially abundant between donors, 44 of which were >0.1% in relative abundance. 17/44 species were enriched in the effective donor, 11 of which (64.7%) were assembled into high-quality genomes that were prevalent (≥75% samples) in that donor, and six showed evidence of engraftment in patients. Taxonomic differences between donors translated to substantial microbial functional differences that were validated using metabolomics.ConclusionDonor microbiota stability and species evenness were identified as novel metrics that were associated with therapeutic efficacy in UC, beyond individual microbial species or metabolites. These metrics may represent community resilience that translates to better engraftment in the host.Trial registration numberACTRN12619000611123.
Traumatic needle damage to nerves during regional anesthesia: presentation of a novel mechanotransduction hypothesis
Authors: McLeod Graeme A , Sadler Amy , Hales Tim G 
Published: July 2022

Despite advances in needle positioning techniques, nerve damage still occurs after regional anesthesia. Recognized causes include local anesthetic toxicity, subperineural injection, high subepineural fluid injection pressures and subepineural hematoma after forceful needle-–nerve contact.We hypothesize that subperineural injection is still possible, but less likely to be the cause of nerve damage because needle penetration of fascicles and mechanical damage is difficult to achieve. High-resolution (75 µm) 40 MHz micro-ultrasound images of pig axillae show short-bevelled 22 g, 0.7 mm wide block needles that are three times larger than the average fascicle. Fascicular bundles are extremely difficult to puncture because they spin away on needle contact. Histology from fresh cadavers after supposed intrafascicular injection shows fluid spread within perineurium and intrafascicular perineural septae, but no breach of endoneurium or axons.We propose that mechanotransduction, the cellular changes that occur in response to force, contributes to nerve damage. Piezo ion channel proteins transduce force into electrical activity by rapid entry of cations into cells. Excessive Ca2+influx into cells has the potential to inhibit nerve regeneration. Cellular changes include regulation of gene expression. The forces associated with purposeful needle insertion are generally unknown. Our experiments in the soft embalmed Thiel cadaver showed a lognormal range of forces between 0.6 N and 16.8 N on epineural penetration.We hypothesize that forceful needle injury may cause nerve damage by activation of Piezo receptors and release of intracellular Ca2+.
Efficient estimation of boundary integrals for path-space differentiable rendering
Authors: Yan Kai , Lassner Christoph , Budge Brian , Dong Zhao , Zhao Shuang 
Published: July 2022

Boundary integrals are unique to physics-based differentiable rendering and crucial for differentiating with respect to object geometry. Under the differential path integral framework---which has enabled the development of sophisticated differentiable rendering algorithms---the boundary components are themselves path integrals. Previously, although the mathematical formulation of boundary path integrals have been established, efficient estimation of these integrals remains challenging.
In this paper, we introduce a new technique to efficiently estimate boundary path integrals. A key component of our technique is a primary-sample-space guiding step for importance sampling of boundary segments. Additionally, we show multiple importance sampling can be used to combine multiple guided samplings. Lastly, we introduce an optional edge sorting step to further improve the runtime performance. We evaluate the effectiveness of our method using several differentiable-rendering and inverse-rendering examples and provide comparisons with existing methods for reconstruction as well as gradient quality.
DEF
Authors: Matveev Albert , Rakhimov Ruslan , Artemov Alexey , Bobrovskikh Gleb , Egiazarian Vage , Bogomolov Emil , Panozzo Daniele , Zorin Denis , Burnaev Evgeny 
Published: July 2022

We propose Deep Estimators of Features (DEFs), a learning-based framework for predicting sharp geometric features in sampled 3D shapes. Differently from existing data-driven methods, which reduce this problem to feature classification, we propose to
regress a scalar field
representing the distance from point samples to the closest feature line on
local patches.
Our approach is the first that scales to massive point clouds by fusing distance-to-feature estimates obtained on individual patches.

We extensively evaluate our approach against related state-of-the-art methods on newly proposed synthetic and real-world 3D CAD model benchmarks. Our approach not only outperforms these (with improvements in Recall and False Positives Rates), but generalizes to real-world scans after training our model on synthetic data and fine-tuning it on a small dataset of scanned data.
We demonstrate a downstream application, where we reconstruct an explicit representation of straight and curved sharp feature lines from range scan data.
We make code, pre-trained models, and our training and evaluation datasets available at https://github.com/artonson/def.
Disentangling random and cyclic effects in time-lapse sequences
Authors: Härkönen Erik , Aittala Miika , Kynkäänniemi Tuomas , Laine Samuli , Aila Timo , Lehtinen Jaakko 
Published: July 2022

Time-lapse image sequences offer visually compelling insights into dynamic processes that are too slow to observe in real time. However, playing a long time-lapse sequence back as a video often results in distracting flicker due to random effects, such as weather, as well as cyclic effects, such as the day-night cycle. We introduce the problem of disentangling time-lapse sequences in a way that allows separate, after-the-fact control of overall trends, cyclic effects, and random effects in the images, and describe a technique based on data-driven generative models that achieves this goal. This enables us to "re-render" the sequences in ways that would not be possible with the input images alone. For example, we can stabilize a long sequence to focus on plant growth over many months, under selectable, consistent weather.
Our approach is based on Generative Adversarial Networks (GAN) that are conditioned with the time coordinate of the time-lapse sequence. Our architecture and training procedure are designed so that the networks learn to model random variations, such as weather, using the GAN's latent space, and to disentangle overall trends and cyclic variations by feeding the conditioning time label to the model using Fourier features with specific frequencies.
We show that our models are robust to defects in the training data, enabling us to amend some of the practical difficulties in capturing long time-lapse sequences, such as temporary occlusions, uneven frame spacing, and missing frames.
Carbohydrate Supplement Impact on Growth Performance, Bacterial Community, and Bacterial Food Quality of Whiteleg Shrimp (Litopenaeus vannamei) under Biofloc System
Authors: Said Mohamed M. , Ahmed Omaima M. 
Published: July 2022

Biofloc technology has a high impact on enhancing shrimp production. Suitable supplemented carbohydrates (CHO) could affect the type of microorganisms developed in the system, which reflects on shrimp production, food safety, and public health. Here, we aimed to compare the effects of sugarcane molasses and wheat flour as carbohydrate sources on biofloc technology. That was achieved through measuring the following parameters: water quality, growth performance, feed utilization, floc composition, shrimp whole body composition, microbial community, and biofloc shrimp food bacterial quality. Postlarvae of whiteleg shrimp (Litopenaeus vannamei) with a mean weight (

38.47
±
5.8

mg

) were stocked at a density of 200 individuals/m2 and cultured under a biofloc system for 128 days in six tanks with a total water volume of 30 m2 each. Water quality analysis revealed a better-dissolved oxygen concentration (5.59 mg/L) in the wheat flour treatment, whereas no significant differences were found between the two treatments in ammonia, nitrite, and pH levels. Increased turbidity (64.27 NTU) and floc volume (18.40 mL/L) were recorded with molasses treatment. Growth performance including final weight, weight gain, average daily gain, weight gain per week, and specific growth rate (12.37 g, 12.34 g, 0.096 g/d, 0.68, and 4.70%, respectively) were all significantly higher in the molasses treatment. Wheat flour treatment was associated with a higher survival rate (99%), biomass (71.16 Kg), and biomass increase percentage (395.337) in shrimps. It also improved feed utilization in terms of a lower feed conversion ratio (1.37) and higher protein efficiency ratio (1.92). The chemical composition of biofloc and shrimp whole body were both nutritious higher in wheat flour treatment. In water, total heterotrophic bacterial counts with sugarcane molasses treatment and wheat flour were estimated as

3.4
×

10

5

CFU
/
mL

and

1.2
×

10

5

CFU
/
mL

, respectively, with no significant difference. In both treatments, beneficial bacteria such as lactic acid bacteria and Enterobacter cloacae were identified in water with the absence of pathogenic Vibrio spp. Wheat flour had a significantly lower total Vibrio-like count (TVC). Shrimps had lower TVC (

1.9
×

10

4

CFU
/
g

) with flour than with molasses (

1.32
×

10

5

CFU
/
g

). Cronobacter spp. were associated with shrimps in BFT supplemented with molasses, which might pose a potential risk to food safety. In conclusion, the use of wheat flour was the best for shrimp production and shrimp food bacterial quality.
And-1 Coordinates with the FANCM Complex to Regulate Fanconi Anemia Signaling and Cisplatin Resistance
Authors: Zhang Yi , Li Jing , Zhou Yuan , Li Zhuqing , Peng Changmin , Pei Huadong , Zhu Wenge 
Published: July 2022

Abstract

The Fanconi anemia (FA) pathway is essential for repairing DNA interstrand crosslinks (ICL). ICLs induce stalled DNA replication forks and trigger activation of the FA pathway by promoting recruitment of the FANCM/FAAP24/MHF complex to ICL sites. Given that stalled replication forks are proximal to ICL sites, fork-associated proteins may coordinate with FA factors to rapidly sense ICLs for activation of FA signaling. Here we report that And-1, a replisome protein, is critical for activation of the FA pathway by sensing ICL-stalled forks and recruiting the FANCM/FAAP24 complex to ICLs. In response to ICLs, And-1 rapidly accumulated at ICL-stalled forks in a manner dependent on ataxia telangiectasia and Rad3-related protein–induced phosphorylation at T826. And-1 phosphorylation triggered an intramolecular change that promoted the interaction of And-1 with FANCM/FAAP24, resulting in recruitment of the FANCM/FAAP24 complex to ICLs. Furthermore, p-T826 And-1 was elevated in cisplatin-resistant ovarian cancer cells, and activated And-1 contributed to cisplatin resistance. Collectively, these studies elucidate a mechanism by which And-1 regulates FA signaling and identify And-1 as a potential target for developing therapeutic approaches to treat platinum-resistant ovarian cancer.

Significance:
This work shows that phosphorylation of And-1 by ATR activates Fanconi anemia signaling at interstrand crosslink–stalled replication forks by recruiting the FANCM/FAAP24 complex, revealing And-1 as a potential therapeutic target in cancer.
Large-Scale In Vitro and In Vivo CRISPR-Cas9 Knockout Screens Identify a 16-Gene Fitness Score for Improved Risk Assessment in Acute Myeloid Leukemia
Authors: Jin Peng , Jin Qiqi , Wang Xiaoling , Zhao Ming , Dong Fangyi , Jiang Ge , Li Zeyi , Shen Jie , Zhang Wei , Wu Shishuang , Li Ran , Zhang Yunxiang , Li Xiaoyang , Li Junmin 
Published: July 2022

Abstract

Purpose:
The molecular complexity of acute myeloid leukemia (AML) presents a considerable challenge to implementation of clinical genetic testing for accurate risk stratification. Identification of better biomarkers therefore remains a high priority to enable improving established stratification and guiding risk-adapted therapy decisions.

Experimental Design:
We systematically integrated and analyzed the genome-wide CRISPR-Cas9 data from more than 1,000 in vitro and in vivo knockout screens to identify the AML-specific fitness genes. A prognostic fitness score was developed using the sparse regression analysis in a training cohort of 618 cases and validated in five publicly available independent cohorts (n = 1,570) and our RJAML cohort (n = 157) with matched RNA sequencing and targeted gene sequencing performed.

Results:
A total of 280 genes were identified as AML fitness genes and a 16-gene AML fitness (AFG16) score was further generated and displayed highly prognostic power in more than 2,300 patients with AML. The AFG16 score was able to distill downstream consequences of several genetic abnormalities and can substantially improve the European LeukemiaNet classification. The multi-omics data from the RJAML cohort further demonstrated its clinical applicability. Patients with high AFG16 scores had significantly poor response to induction chemotherapy. Ex vivo drug screening indicated that patients with high AFG16 scores were more sensitive to the cell-cycle inhibitors flavopiridol and SNS-032, and exhibited strongly activated cell-cycle signaling.

Conclusions:
Our findings demonstrated the utility of the AFG16 score as a powerful tool for better risk stratification and selecting patients most likely to benefit from chemotherapy and alternative experimental therapies.
A survey of exact motif finding algorithms
Authors: Yousif Ali Basim , Keitan Al-Khafaji Hussein , Abbas Thekra 
Published: July 2022

<span lang="EN-US"><span lang="EN-US">Deoxyribonucleic </span>acid (DNA) motif finding (discovery/mining) in biological chains is the most recent challenging and interesting trend in bioinformatics. It represents a crucial phase in most bioinformatics systems related to unravelling the secrets of gene functions. Despite the efforts made to date to produce robust algorithms, DNA motif finding remains a difficult task for researchers in this field. In general, biological pattern locating algorithms are categorized into two categories: probabilistic and numerical methods. In this paper, we provide a survey of exact DNA motif finding algorithms and their working principles with a suitable comparison among these algorithms to provide an essential step for researchers in this field.</span>
Classification of focal liver disease in egyptian patients using ultrasound images and convolutional neural networks
Authors: Abd-ElGhaffar Rania Mohamed , El-Zalabany Mahmoud , El-Din Moustafa Hossam , El-Seddek Mervat 
Published: July 2022

Recently, <span>computer-aided diagnostic systems for various diseases have received great attention. One of the latest technologies used is deep learning architectures for analyzing and classifying medical images. In this paper, a new system that uses deep learning to classify three focal diseases in the liver besides the normal liver is proposed. A pre-trained convolutional neural network is utilized. Two types of networks are used, ResNet50 and AlexNet with fully connected networks (FCNs). After extracting the deep features using deep learning, FCNs can input images in different states of the disease, such as Normal, Hem, HCC, and Cyst. Dataset is obtained from the Egyptian Liver Research Institute. Two classifiers are utilized, the first includes two classes (Normal/Cyst, Normal/Hem, Normal/HCC, HCC/Cyst, HCC/Hem, Cyst/Hem) and the second contains four classes (Normal/Cyst/ HCC/Hem) to distinguish liver images. Using performance criteria, it has been shown that the two-category classifiers have given better results than the four-class classifier, and accordingly a hybrid classifier was suggested to merge the weighted probabilities of the classes obtained by each singular classifier. Experimental results have achieved an accuracy of 96.1% using ResNet50 which means that it can be used as an assistive diagnostic method for classification of focal liver disease.</span>
Blockchain adoption barriers in Moroccan sustainable supply chain: a proposed approach
Authors: Bendarag Abdesadik , Boutkhoum Omar , Abada Driss , Hanine Mohamed 
Published: July 2022

Currently, <span>the emerging countries like Morocco seeks to benefit from the potential of blockchain technology to meet its various growing demands, especially in sustainable supply chain management (SSCM). This explains the need for more effort to understand blockchain implementation and identify the barriers influencing the blockchain adoption decision in SSCM, especially, from Moroccan industry and service sectors perspective. In this context, this research paper proposes a group decision-making approach to identify the barriers from a comprehensive literature search, then evaluate them based on intuitionistic fuzzy analytic hierarchy process (IFAHP). Due to the varied importance of the selected barriers, IFAHP is utilized to allocate priority weights for each barrier according to its importance level. The evaluation results reveal that “Government policy and support” and “Challenges in integrating sustainable practices and blockchain technology through <a name="_Hlk106113265"></a>sustainable supply chain management (SCM)” are the best ranked barriers that impact the implementation of blockchain technology in Moroccan context. The main objective is to inquire the barriers preventing the blockchain implementation, and assist industry decision-makers in developing supple short- and long-term decision-making strategies for better sustainable supply chain management.</span>