bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semantic annotation for computational pathology: multidisciplinary experience and best practice recommendations
Authors: Wahab Noorul , Miligy Islam M , Dodd Katherine , Sahota Harvir , Toss Michael , Lu Wenqi , Jahanifar Mostafa , Bilal Mohsin , Graham Simon , Park Young , Hadjigeorghiou Giorgos , Bhalerao Abhir , Lashen Ayat G , Ibrahim Asmaa Y , Katayama Ayaka , Ebili Henry O , Parkin Matthew , Sorell Tom , Raza Shan E Ahmed , Hero Emily , Eldaly Hesham , Tsang Yee Wah , Gopalakrishnan Kishore , Snead David , Rakha Emad , Rajpoot Nasir , Minhas Fayyaz 
Published: January 2022

AbstractRecent advances in whole‐slide imaging (WSI) technology have led to the development of a myriad of computer vision and artificial intelligence‐based diagnostic, prognostic, and predictive algorithms. Computational Pathology (CPath) offers an integrated solution to utilise information embedded in pathology WSIs beyond what can be obtained through visual assessment. For automated analysis of WSIs and validation of machine learning (ML) models, annotations at the slide, tissue, and cellular levels are required. The annotation of important visual constructs in pathology images is an important component of CPath projects. Improper annotations can result in algorithms that are hard to interpret and can potentially produce inaccurate and inconsistent results. Despite the crucial role of annotations in CPath projects, there are no well‐defined guidelines or best practices on how annotations should be carried out. In this paper, we address this shortcoming by presenting the experience and best practices acquired during the execution of a large‐scale annotation exercise involving a multidisciplinary team of pathologists, ML experts, and researchers as part of the Pathology image data Lake for Analytics, Knowledge and Education (PathLAKE) consortium. We present a real‐world case study along with examples of different types of annotations, diagnostic algorithm, annotation data dictionary, and annotation constructs. The analyses reported in this work highlight best practice recommendations that can be used as annotation guidelines over the lifecycle of a CPath project.
Image2SMILES: Transformer‐Based Molecular Optical Recognition Engine**
Authors: Khokhlov Ivan , Krasnov Lev , Fedorov Maxim V. , Sosnin Sergey 
Published: January 2022

AbstractThe rise of deep learning in various scientific and technology areas promotes the development of AI‐based tools for information retrieval. Optical recognition of organic structures is a key part of the automated extraction of chemical information. However, this is a challenging task because there is a large variety of representation styles. In this research, we present a Transformer‐based artificial neural network to convert images of organic structures to molecular structures. To train the model, we created a comprehensive data generator that stochastically simulates various drawing styles, functional groups, functional group placeholders (R‐groups), and visual contamination. We demonstrate that the Transformer‐based architecture can gather chemical insights from our generator with almost absolute confidence. That means that, with Transformer, one can fully concentrate on data simulation to build a good recognition model. A web demo of our optical recognition engine is available online at Syntelly platform, and the code for dataset generation is available on GitHub.
Cooperative Effect of Noncovalent Interactions on Tetrel Bonding in Halogenated Silanes
Authors: Khera Mayank , Goel Neetu 
Published: January 2022

AbstractTetrel bond, a weak noncovalent interaction between the σ‐hole of a Group IV element (silicon in our case) and the cloud of an electronegative element (oxygen in our case) is the focus of this work. The percentage strengthening of tetrel bond has been investigated by optimizing 16 binary complexes of halogenated silane and water of general formula SiXnH4−n−H2O and 16 ternary complexes, of general formula NaX−SiXnH4−n−H2O, where X=F, Cl, Br and I and n=1, 2, 3 and 4 at various levels of theory defined within the formalism of density functional theory (DFT). With the addition of NaX, tetrel bond between Si and O in SiXnH4−n−H2O gets strengthened up to 49 %, owing to cooperativity effect exerted by hydrogen bonding between X and H in the ternary complex NaX−SiXnH4−n−H2O. In the series of complexes studied here, overall stabilization due to cooperativity lies between 10 kJ/mol to 170 kJ/mol. This large extent of reinforcement due to cooperativity has never been showcased before. The exceptional stabilization and reinforcement owe its genesis to the transformation of the ternary complex into a cluster orchestrated by the H‐bonding in most of the cases and covalent bonding in few of the cases.
Genetic Approaches to Weed Control
Authors: Sever Megan 
Published: January 2022

AbstractWeeds have evolved quicker than our ways to eradicate them with 264 species of weeds worldwide developing resistance to herbicides. Genetic weed control is one option being looked at by researchers. There are a number of hurdles to overcome before this approach could be used, including ethical, regulatory, and ecological challenges, but it is an area of research that may be worth pursuing. Earn 1 CEU in Integrated Pest Management by reading the article and taking the quiz at https://bit.ly/3lDTorO. View all CEUs online at https://web.sciencesocieties.org/Learning‐Center/Courses.
Amide Bonds Meet Flow Chemistry: A Journey into Methodologies and Sustainable Evolution
Authors: Alfano Antonella Ilenia , Lange Heiko , Brindisi Margherita 
Published: January 2022

AbstractFormation of amide bonds is of immanent importance in organic and synthetic medicinal chemistry. Its presence in “traditional” small‐molecule active pharmaceutical ingredients, in linear or cyclic oligo‐ and polypeptidic actives, including pseudopeptides, has led to the development of dedicated synthetic approaches for the formation of amide bonds starting from, if necessary, suitably protected amino acids. While the use of solid supported reagents is common in traditional peptide synthesis, similar approaches targeting amide bond formation in continuous‐flow mode took off more significantly, after a first publication in 2006, only a couple of years ago. Most efforts rely upon the transition of traditional approaches in flow mode, or the combination of solid‐phase peptide synthesis principles with flow chemistry, and advantages are mainly seen in improving space‐time yields. This Review summarizes and compares the various approaches in terms of basic amide formation, peptide synthesis, and pseudopeptide generation, describing the technological approaches and the advantages that were generated by the specific flow approaches. A final discussion highlights potential future needs and perspectives in terms of greener and more sustainable syntheses.
Design and investigation of a triple boost multilevel inverter with self‐balanced switched capacitors and reduced voltage stress
Authors: Sarwer Zeeshan , Anwar Md Nishat , Sarwar Adil 
Published: January 2022

AbstractMultilevel inverters (MLI) play a key role in various medium voltage and high power industrial applications. This paper proposes a triple boost multilevel inverter (TBMLI) comprising switched capacitors. The special features of the proposed circuit are three times boosted output voltage, reduced voltage stress on switches, and the presence of a single dc source. Moreover, the self‐balancing in the capacitors voltage which eliminates the need of auxiliary control circuitry and reduced number of overall components also add to the salient qualities of proposed MLI. The simulation has been done using MATLAB/Simulink, whereas the loss analysis, describing the distribution of the various power loss, has been completed with the help of PLECS software. The proposed topology has a maximum efficiency of 98.3%, whereas the THD in output voltage is 13.65%. The proposed MLI is experimentally investigated to see its performance. A comparison has been conducted to assess the proposed MLI on various parameters.
Comparison of the tumor microenvironments of squamous cell carcinoma at different anatomical locations within the upper aerodigestive tract in relation to response to ICI therapy
Authors: van Duijvenvoorde Maurice , Derks Sarah , Bahce Idris , Leemans C René , van de Ven Rieneke , Fransen Marieke F 
Published: January 2022

AbstractImmunotherapy with immune checkpoint inhibitors (ICI) has improved treatment outcomes in many cancer types and has focused attention on cancer immunity and the role of the tumor microenvironment (TME). Studies into efficacy of immunotherapy and TME are generally restricted to tumors in one anatomical location, while the histological type may have substantial influence on the contexture of the TME, perhaps more so than anatomical location, and subsequently to the response to immunotherapy. This review aims to focus on the TME in ICI‐treated tumors of the same histological type, namely carcinogen‐induced squamous cell carcinoma developing within the aerodigestive tract, at three locations, i.e. head and neck (HNSCC), esophagus (ESCC) and lung (LUSC).
Underwater endoscopic mucosal resection for colorectal lesions: Can it be an “Underwater” revolution?
Authors: Takeuchi Yoji , Shichijo Satoki , Uedo Noriya , Ishihara Ryu 
Published: January 2022

AbstractUnderwater endoscopic mucosal resection (UEMR) is a newly developed technique for the removal of colorectal, duodenal, esophageal, gastric, ampullary, and small intestinal lesions. We performed a PubMed literature search for articles reporting UEMR outcomes for colorectal polyps. Four randomized controlled trials, nine non‐randomized prospective trials, 16 retrospective studies, and 27 case reports were selected for assessment of the efficacy and safety of UEMR. We summarized the therapeutic outcomes of UEMR in each category according to the lesion characteristics [small size (<10 mm), intermediate size (10–19 mm), large size (≥20 mm), recurrent lesion, and rectal neuroendocrine tumor], and calculated the incidence of adverse events among the included articles. As the treatment outcomes for small polyps appeared similar between UEMR and conventional endoscopic mucosal resection (CEMR), UEMR can be a standard procedure for small colorectal polyps suspicious for high‐grade dysplasia to avoid incomplete removal of occult invasive cancer by cold snare polypectomy. As UEMR showed satisfactory outcomes for intermediate‐size lesions and recurrent lesions after endoscopic resection, UEMR can be a standard procedure for these lesions. Regarding large lesions and rectal neuroendocrine tumors, comparisons of UEMR with current standard methods for them were lacking, and further investigations are warranted. Adverse events appeared comparable or less frequent for UEMR compared with CEMR but still existed. Therefore, careful implementation of this new technique in clinical practice is important for its widespread use.
Visibility evaluation of colorectal lesion using texture and color enhancement imaging with video
Authors: Tamai Naoto , Horiuchi Hideka , Matsui Hiroaki , Furuhashi Hiroto , Kamba Shunsuke , Dobashi Akira , Sumiyama Kazuki 
Published: January 2022

AbstractObjectiveTo evaluate the visibility of colorectal lesions using a novel image processing algorithm, texture and color enhancement imaging (TXI), that allows the acquisition of brighter images with enhanced color and surface structure.MethodsDuring August–September 2019, patients referred for endoscopic treatment were prospectively recruited. Electronic data acquired while observing colorectal lesions using white light imaging (WLI) were obtained and recorded: WLI, TXI mode1 (with color enhancement), and TXI mode2 (without color enhancement) videos were constructed. The lesions were also recorded using narrow‐band imaging (NBI) from the same perspective as WLI. Four video clips (WLI, TXI mode1, TXI mode2, and NBI) were made per lesion. Thereafter, video files for evaluations were prepared by randomly arranging all video clips. Finally, visualization scores were evaluated by four endoscopists, and the WLI, TXI mode1, TXI mode2, and NBI results were compared.ResultsOverall, 22 patients with 68 lesions were recruited; the video file for evaluation subsequently comprised 272 randomly arranged video clips. Mean visualization scores using WLI, TXI mode1, TXI mode2, and NBI were 70.0 (±20.1), 80.5 (±18.6), 75.6 (±18.1), and 69.0 (±20.6), respectively. Mean visualization scores for flat lesions using WLI, TXI mode1, TXI mode2, and NBI were 64.1 (±21.2), 76.5 (±20.18), 71.8 (±19.4), and 64.2 (±22.0), respectively. Visualization scores using TXI mode1 were significantly better than those using WLI, TXI mode2, or NBI.ConclusionsTXI enables improved visualization of colorectal lesions, even flat lesions, than WLI and NBI. TXI may allow better detection of colorectal lesions, although further prospective studies are required.
Effects of intraspecific competition and body mass on diet specialization in a mammalian scavenger
Authors: Lewis Anna C. , Hughes Channing , Rogers Tracey L. 
Published: January 2022

AbstractAnimals that rely extensively on scavenging rather than hunting must exploit resources that are inherently patchy, dangerous, or subject to competition. Though it may be expected that scavengers should therefore form opportunistic feeding habits in order to survive, a broad species diet may mask specialization occurring at an individual level. To test this, we used stable isotope analysis to analyze the degree of specialization in the diet of the Tasmanian devil, one of few mammalian species to develop adaptations for scavenging. We found that the majority of individuals were dietary specialists, indicating that they fed within a narrow trophic niche despite their varied diet as a species. Even in competitive populations, only small individuals could be classified as true trophic generalists; larger animals in those populations were trophic specialists. In populations with reduced levels of competition, all individuals were capable of being trophic specialists. Heavier individuals showed a greater degree of trophic specialization, suggesting either that mass is an important driver of diet choice or that trophic specialization is an efficient foraging strategy allowing greater mass gain. Devils may be unique among scavenging mammals in the extent to which they can specialize their diets, having been released from the competitive pressure of larger carnivores.
Parasites in kelp‐forest food webs increase food‐chain length, complexity, and specialization, but reduce connectance
Authors: Morton Dana N. , Lafferty Kevin D. 
Published: January 2022

AbstractWe explored whether parasites are important in kelp forests by examining their effects on a high‐quality, high‐resolution kelp‐forest food web. After controlling for generic effects of network size, parasites affected kelp‐forest food web structure in some ways consistent with other systems. Parasites increased the trophic span of the web, increasing top predator vulnerability and the longest chain length. Unique links associated with parasites, such as concomitant predation (consumption of parasites along with their hosts by predators) increased the frequency of network motifs involving mutual consumption and decreased niche contiguity of free‐living species. However, parasites also affected kelp‐forest food web structure in ways not seen in other systems. Kelp‐forest parasites are richer and more specialized than other systems. As a result, parasites reduced diet generality and decreased connectance in the kelp forest. Although mutual consumption motifs increased in frequency, this motif type was still a small fraction of all possible motifs, so their increase in frequency was not enough to compensate for the decrease in connectance caused by adding many specialist parasite species.
On the origin of feces: Fungal diversity, distribution, and conservation implications from feces of small mammals
Authors: Bradshaw Alexander J. , Autumn Kendra C. , Rickart Eric A. , Dentinger Bryn T. M. 
Published: January 2022

AbstractFungi are highly diverse, but only a small fraction of the total estimated species have been characterized. Often, the extent of diversity and distribution of fungal communities is difficult or near impossible to assess due to the fact that many fungi are cryptic and persist predominantly hidden within substrates such as soil or plant material. This is particularly true for hypogeous sporocarps, such as truffles and false truffles, which are extremely difficult to survey in a systematic manner. However, hypogeous fungi have evolved traits that make them highly attractive to animals, such as small mammals, which ingest and disperse fungal spores through defecation. Here, samples of feces from 138 small mammal museum vouchers collected in the western United States were assessed for total fungal diversity using a dual‐index metabarcoding approach. Our findings exhibit many identifications within the mushroom‐forming fungi (Agaricomycetidae), with 65 of the 138 samples containing sequences belonging to several species of the false truffle‐forming genus Rhizopogon. Metadata for each collection, such as geospatial coordinates, can be used as a proxy for the presence or absence of Rhizopogon species identified in their feces. Utilizing these proxy data from only a few years of sampling, these records quadrupled the rate of observations of Rhizopogon made over the past 100 years, including some species that have only been recorded once previously. This substantial increase in datapoints has implications for how fungal distributions are interpreted, with direct impact on standard assessment tools for fungal conservation.
First‐in‐human experience of preload regulation with percutaneous transluminal caval flow regulation in heart failure with reduced ejection fraction patients
Authors: Herrera José E. , Herrera José A. , Finizola Bartolomé , García Eleazar , Velasco Luis E. , Torres William R. , D'empaire Gabriel , Octavio José A. , Marqués Juan A. , Levine Robert A. , Palacios Igor F. 
Published: January 2022

AbstractAimsThis study aims to investigate the acute haemodynamic effects of percutaneous transluminal flow regulation (PTCR®) with an inferior vena cava regulator balloon in heart failure patients. Preload reduction in heart failure has been achieved with high potency diuretics. However, no study has been conducted in humans to assess the effect of inferior vena cava intermittent occlusion for preload reduction.Methods and resultsSix patients were included in the study: four men (55 ± 6 years old) and two women (63 ± 4 years old). Baseline evaluations included Doppler echocardiogram, coronary angiogram, and right heart catheterization. Caval balloon was kept inflated for 30 min, and right catheterization and control echocardiogram were performed while the balloon was still inflated. The balloon was then deflated and removed. Right haemodynamic variables were evaluated before balloon insertion and with the inflated balloon. The mean right atrial pressure decreased by 42.59% (P = 0.005); systolic right ventricular pressure decreased by 30.19% (P < 0.003); mean pulmonary arterial pressure decreased by 25.33% (P < 0.043); mean pulmonary capillary wedge pressure decreased by 31.37% (P > 0.016); and cardiac output increased by 9.92% (P < 0.175).ConclusionsThe haemodynamic and echocardiographic changes obtained in our study using PTCR® suggest that this innovative approach can play a beneficial role in the heart failure treatment.
A Convenient Synthesis of Fluoroalkylated Benzimidazole‐ or Indole‐fused Benzoxazines
Authors: Hu Yijie , Wang Xiaoli , Ren Nan , Li Na , Li Jianyang , Chen Jie , Zhang Hui , Deng Hongmei , Cao Weiguo , Lin Jin‐Hong 
Published: January 2022

AbstractFluoroalkyl group is of particular interest in pharmaceutical chemistry. Since benzimidazole‐ or indole‐fused benzoxazines are important motifs in numerous biologically active molecules, the incorporation of a fluoroalkyl group into these molecules may provide more opportunities for drug developments. Herein we describe the first synthesis of fluoroalkylated benzimidazole‐ or indole‐fused benzoxazines by using fluoroalkylated propiolates as building blocks. The reactions proceeded smoothly under mild conditions to give the desired products in moderate to high yields. Notably, benzimidazole‐fused products were obtained by a convenient one‐pot two‐step process.
Synthesis of 2‐Substituted Indoles by Pd‐Catalyzed Reductive Cyclization of 1‐Halo‐2‐nitrobenzene with Alkynes
Authors: Lokolkar Manjunath S. , Mane Pravin A. , Dey Sandip , Bhanage Bhalchandra M. 
Published: January 2022

AbstractAn effective process for synthesizing 2‐substituted indoles in a one‐pot tandem reaction of 1‐halo‐2‐nitrobenzene and terminal alkynes through addition/reductive cyclization is presented. This protocol involves a Sonogashira‐type coupling reaction followed by reductive cyclization employing dppf (1,1′‐bis(diphenylphosphino)ferrocene) ligated Pd dithiolate complex as a catalyst and Zn as an inexpensive reductant. This efficient and tandem process tolerates broad functional groups with moderate to good yields. The gram‐scale synthesis of 2‐substituted indole has also been demonstrated. This protocol provides an alternative route for the synthesis of 2‐substituted indoles.
Prediction of effective vibration condition under air void reduction using mortar rheological constant
Authors: Kisaku Tomoaki , Yoshida Yuki , Muto Kaho , Kurosawa Takashi , Ito Yuji , Fujiyama Chikako 
Published: January 2022

AbstractAir voids remaining on the concrete surface are detrimental to the durability. Surface voids also affect the esthetics of concrete structures. In this study, the method of reducing the surface voids caused by entrapped air of fresh concrete was verified using 122 cases of vibration box tests with different materials, mix proportions, vibration frequencies, and amplitudes. The surface void area ratio (SVAR) decreased when the acceleration of the vibration box was increased regardless of the type of concrete. The relationship between SVAR and acceleration can be expressed through a power function. However, a segregation was observed in medium‐fluidity concrete when the acceleration exceeded 4.0 Gal (hereinafter referred to as G). In addition, the SVAR correlated with the mortar rheological constant was measured using a steel ball pull‐up test. An equation using mortar rheological constants, which can be estimated using a concrete slump, was proposed to predict the SVAR‐acceleration relationship.