bluuebunny/crossref_metadata_2025 huggingface dataset:
A class of high-order improved fast weighted essentially non-oscillatory schemes for achieving optimal order at any critical points
Authors: Zhang Xin , Huang Lintao , Jiang Zhenhua , Yan Chao
Published: November 2022

The weighted essentially non-oscillatory (WENO) scheme is one of the most popular shock-capturing schemes, and constructing a more efficient and higher-order WENO scheme has always been an intention of optimization design. In the general WENO reconstruction framework, the smoothness indicator plays an important role in identifying whether the sub-stencils are in discontinuous or smooth regions. However, the classical smoothness indicator is the most expensive one in the whole reconstruction algorithm, and its computational complexity increases sharply with the improvement of the accuracy order. Therefore, a class of efficient and superior WENO schemes called improved fast WENO (IFWENO) are proposed based on the fast WENO (FWENO). To improve efficiency, the smoothness indicator of the IFWENO scheme is simplified from the traditional version, and the nonlinear weight calculation method is modified. The parameter ε is carefully designed to obtain the superior property that the accuracy of the spatial derivatives will not degrade at any order critical point in smooth regions. The reason for the instability occurring in the high-order FWENO is revealed, and the parameter p is likewise specifically selected to improve robustness at discontinuities. The excellent multi-scale resolution of the proposed IFWENO scheme is proven by theoretical analyses and numerical experiments. Through several typical examples, the consistently high accuracy and efficiency of the designed scheme in both smooth and discontinuous regions are verified.
An exploration of the inverse care law and market forces in Australian primary health care
Authors: Harris Elizabeth , Harris Mark F.
Published: November 2022

This paper examines the implications of the second sentence in Tudor Harts statement about inverse care – that its operation was strongest when exposed to market forces. In the Australian context, we briefly review some available evidence for inverse care in three groups – Aboriginal and Torres Strait Islander people and those living in remote and socioeconomically disadvantaged areas. We then discuss the extent to which these examples can be attributed to the operation of supply-and-demand within Australia’s hybrid fee-for-service system in general practice. Our analysis suggests disparities in workforce supply and the ability of disadvantaged groups to seek preventive and proactive care are critical factors. These, in turn, suggest the need to fund general practice to be responsible for proactive and preventive care of disadvantaged population groups alongside broader structural reforms in workforce, education and taxation.
Persistent organic pollutants affect steroidogenic and apoptotic activities in granulosa cells and reactive oxygen species concentrations in oocytes in the mouse
Authors: Krawczyk Kinga , Marynowicz Weronika , Pich Karolina , Jędruch Oliwia , Kania Gabriela , Gogola-Mruk Justyna , Tworzydło Wacław , Polański Zbigniew , Ptak Anna
Published: November 2022

Context The destruction of granulosa cells (GCs), the main functional cell type in the ovary, prevents steroid hormone production, which in turn may damage oocytes, resulting in ovarian failure. The accumulation of a number of persistent organic pollutants (POPs) in the ovarian follicular fluid (FF) has been documented, which raises serious questions regarding their impact on female fertility. Aims We aimed to determine whether a mixture of POPs reflecting the profile found in FF influences mouse GCs or oocyte function and viability. Methods A mixture of POPs, comprising perfluorooctanoate, perfluorooctane sulfonate, 2,2-dichlorodiphenyldichloroethylene, polychlorinated biphenyl 153, and hexachlorobenzene, was used. In addition to using the exact concentration of POPs previously measured in human FF, we tested two other mixtures, one with10-fold lower and another with 10-fold higher concentrations of each POP. Key results Steroidogenesis was disrupted in GCs by the POP mixture, as demonstrated by lower oestradiol and progesterone secretion and greater lipid droplet accumulation. Furthermore, the POP mixture reduced GC viability and increased apoptosis, assessed using caspase-3 activity. The POP mixture significantly increased the number of oocytes that successfully progressed to the second meiotic metaphase and the oocyte reactive oxygen species (ROS) concentration. Conclusions Thus, a mixture of POPs that are typically present in human FF has detrimental effects on ovarian function: it reduces the viability of GCs, and increases the oocyte concentrations of ROS. Implications These results indicate that chronic exposure to POPs adversely affects female reproductive health.
Effect of melatonin and nitric oxide on capacitation and apoptotic changes induced by epidermal growth factor in ram sperm
Authors: Miguel-Jiménez Sara , Carvajal-Serna Melissa , Peña-Delgado Victoria , Casao Adriana , Pérez-Pe Rosaura
Published: November 2022

Context Apart from the canonical cAMP-PKA pathway, ram sperm capacitation can be achieved by the MAPK ERK1/2 signalling cascade, activated by epidermal growth factor (EGF). Aims This study aims to investigate the effect of melatonin and nitric oxide (NO·) on capacitation and apoptotic-like changes in EGF-capacitated ram spermatozoa. Methods In vitro capacitation was induced by EGF in the absence or presence of melatonin (100 pM or 1 μM). Also, a NO· precursor, L-arginine, or a NOS inhibitor, NG-nitro-L-arginine methyl ester (L-NAME), were added to capacitation media to study the interaction of NO· and melatonin during EGF-capacitation. Sperm functionality parameters (motility, viability, capacitation state), apoptotic markers (caspase activation and DNA damage), NO· levels, and phosphorylated c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (assessed by Western blot), were evaluated in swim-up and capacitated samples with EGF. Key results NO· levels and the apoptotic-related markers were raised after EGF incubation. Melatonin had a bimodal role on sperm EGF-capacitation, preventing it at high concentration and promoting acrosome reaction at low concentration, but neither of the two concentrations prevented the increase in apoptotic-like markers or NO· levels. However, melatonin at 1 μM prevented the activation of JNK. Conclusions NO· metabolism does not seem to modulate the apoptosis-like events in ram spermatozoa. Melatonin at 1 μM prevents ram sperm capacitation induced by EGF independently from nitric oxide metabolism, and it could be exerted by limiting the JNK mitogen-activated protein kinase (MAPK) activation. Implications This study improves our understanding of the biochemical mechanisms involved in sperm capacitation, and ultimately, fertility.
Multivariate analysis of hydropedologically significant soil variables on cultivated semi-arid hillslopes
Authors: Kavaklıgil Seval Sünal , Erşahin Sabit
Published: November 2022

Context Hydropedology bridges hydrology to pedology, and hillslope hydropedology is central in understanding topography–hydropedology interrelations. Aim The objective of this study was to statistically evaluate soil–hillslope hydropedology interrelations by multivariate analysis of hydropedologically significant soil variables (HSSVs). Methods A complete randomised 6 × 5 × 3 factorial experiment (six slope aspects, five slope positions and three soil horizons) was established. Twenty nine soil profiles were excavated and described on topslope, shoulder, backslope, footslope, and toeslope positions of hillslopes oriented in different directions. A total of 486 soil samples were taken from A, B, and C horizons at 174 sampling points and analysed for soil parametric properties. In addition, soil morphometric factors were described in the field and converted to their quantitative values. Relationships among HSSVs were analysed by Spearman’s correlation and principal component analysis. Association between HSSVs, soil horizonation and slope factors (slope aspect and position) was analysed by a multivariate factorial ANOVA. Results Slope aspect and slope position were dominant factors, which significantly affected (P < 0.05) variability in the majority of the HSSVs. Variability in clay and sand contents, bulk density, organic matter content, saturated hydraulic conductivity, and field capacity was significantly affected (P < 0.05) by these factors. Also, soil morphological variables of concentration factors (such as clay accumulation on the ped faces and pore walls), mottles, rupture resistance, stickiness, and plasticity were significantly (P < 0.05) controlled by these factors. Conclusions Clay content and abundance of concentration factors must be included in prospective similar studies, as they are key soil indicators of hydropedology. Implications Further studies should be conducted with different soils for an improved conceptualisation of hillslope-hydropedology interrelations.
Detecting burnt severity and vegetation regrowth classes using a change vector analysis approach: a case study in the southern part of Sumatra, Indonesia
Authors: Santi Nitya Ade , Jaya I Nengah Surati , Saleh Muhammad Buce , Syaufina Lailan , Kuncahyo Budi
Published: November 2022

This study describes the development of burn severity and vegetation regrowth classes using vegetation (NDVI) and bareland (NDBI) indices-based change vector analysis (VI-CVA) with a case study on the fire event that occurred at the Berbak National Park, Jambi Province, in 2015. The main objective was to determine the type and the severity level of change due to fire or vegetation regrowth, as summarised in CVA magnitude and direction images. The vegetation and bareland indices were derived from Landsat medium-resolution images to detect the degree of change caused by the forest fires. The study found that severity and vegetation regrowth could be classified into five classes: unburnt, very low, low, and moderate severity burn classes and a moderate regrowth class from bare land to oil palm plantation, and unburnt. It was also found that the performance of this CVA approach was superior to the delta normalized burn ratio (dNBR) method as indicated by its ability to detect five post-fire severity classes with 87.7% overall accuracy compared with dNBR, which detected four post-fire severity classes with 66.9% overall accuracy.
Formation of tantalum coatings with a given structure on the surface of niti alloy by magnetron sputter deposition
Authors: Larionov А S , Dikov А S , Akayev S О , Dikova L А , Zhakanbayev Е А , Sarsenbaeva К B
Published: November 2022

Way for applying tantalum coating with a given structure to the surface of an alloy with a shape memory effect NiTi to increase the biocompatibility of implants from this alloy is presented. The coating was synthesized by direct current (DC) magnetron sputtering. The changes sequence of the structural-phase states depending on the thickness of the coating, that is, the rate of its deposition, has been established. It is shown that at a low magnetron power, ∼14 W in present study, a single-phase α-Ta coating with a bcc structure and a high degree of perfection of the crystal lattice is successfully synthesized on the titanium nickelide surface.
Medicine and Health “in the Least Civilized Regions”
Authors: Carey David
Published: November 2022

In nations with large Indigenous populations like Guatemala and Ecuador, overlapping narratives of nationalism, public health, and race signal the complexity of modernizing health care. Various variables—race, gender, class, geography, the role of the state, divisions within the ruling class—impinged on people’s health care decisions. To analyze how racial thought and public health influenced each other during Guatemala’s predominantly dictatorial rule and Ecuador’s authoritarian but more participatory government at a time when the most significant international public health organization—the Rockefeller Foundation (RF)—sought to improve public health in both countries, I combine transnational and comparative historical analyses of the first half of the twentieth century. Triangulating Guatemalan, Ecuadorian, and RF archives and focusing on the primacy of Indigenous voices reveals an interactive matrix of different types of racism in Guatemala, Ecuador, and RF that shaped indígenas’ (Indigenous people’s) engagement with, exclusion from, or rejection of public health initiatives and scientific medicine. The politics of indigeneity was as consequential for public health as scientific developments. Many state agents and RF representatives used public health contexts to mobilize social constructions of race and ethnicity that advanced their agendas and marginalized indígenas. In turn, indígenas often determined the extent to which authorities’ aspirations matched their accomplishments.
IPPF-FE: an integrated peptide and protein function prediction framework based on fused features and ensemble models
Authors: Yu Han , Luo Xiaozhou
Published: November 2022

The prediction of peptide and protein function is important for research and industrial applications, and many machine learning methods have been developed for this purpose. The existing models have encountered many challenges, including the lack of effective and comprehensive features and the limited applicability of each model. Here, we introduce an Integrated Peptide and Protein function prediction Framework based on Fused features and Ensemble models (IPPF-FE), which can accurately capture the relationship between features and labels. The results indicated that IPPF-FE outperformed existing state-of-the-art (SOTA) models on more than 8 different categories of peptide and protein tasks. In addition, t-distributed Stochastic Neighbour Embedding demonstrated the advantages of IPPF-FE. We anticipate that our method will become a versatile tool for peptide and protein prediction tasks and shed light on the future development of related models. The model is open source and available in the GitHub repository https://github.com/Luo-SynBioLab/IPPF-FE.
Label-free proteome quantification and evaluation
Authors: Fu Jianbo , Yang Qingxia , Luo Yongchao , Zhang Song , Tang Jing , Zhang Ying , Zhang Hongning , Xu Hanxiang , Zhu Feng
Published: November 2022

The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on >3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.
HN-PPISP: a hybrid network based on MLP-Mixer for protein–protein interaction site prediction
Authors: Kang Yan , Xu Yulong , Wang Xinchao , Pu Bin , Yang Xuekun , Rao Yulong , Chen Jianguo
Published: November 2022

Motivation

Biological experimental approaches to protein–protein interaction (PPI) site prediction are critical for understanding the mechanisms of biochemical processes but are time-consuming and laborious. With the development of Deep Learning (DL) techniques, the most popular Convolutional Neural Networks (CNN)-based methods have been proposed to address these problems. Although significant progress has been made, these methods still have limitations in encoding the characteristics of each amino acid in protein sequences. Current methods cannot efficiently explore the nature of Position Specific Scoring Matrix (PSSM), secondary structure and raw protein sequences by processing them all together. For PPI site prediction, how to effectively model the PPI context with attention to prediction remains an open problem. In addition, the long-distance dependencies of PPI features are important, which is very challenging for many CNN-based methods because the innate ability of CNN is difficult to outperform auto-regressive models like Transformers.

Results

To effectively mine the properties of PPI features, a novel hybrid neural network named HN-PPISP is proposed, which integrates a Multi-layer Perceptron Mixer (MLP-Mixer) module for local feature extraction and a two-stage multi-branch module for global feature capture. The model merits Transformer, TextCNN and Bi-LSTM as a powerful alternative for PPI site prediction. On the one hand, this is the first application of an advanced Transformer (i.e. MLP-Mixer) with a hybrid network for sequence-based PPI prediction. On the other hand, unlike existing methods that treat global features altogether, the proposed two-stage multi-branch hybrid module firstly assigns different attention scores to the input features and then encodes the feature through different branch modules. In the first stage, different improved attention modules are hybridized to extract features from the raw protein sequences, secondary structure and PSSM, respectively. In the second stage, a multi-branch network is designed to aggregate information from both branches in parallel. The two branches encode the features and extract dependencies through several operations such as TextCNN, Bi-LSTM and different activation functions. Experimental results on real-world public datasets show that our model consistently achieves state-of-the-art performance over seven remarkable baselines.

Availability

The source code of HN-PPISP model is available at https://github.com/ylxu05/HN-PPISP.
Muscarinic and NMDA Receptors in the Substantia Nigra Play a Role in Reward-Related Learning
Authors: Galaj Ewa , Barrera Eddy D , Lynch Olivia L , Diodati Rachel , Thomas Ashley , Schneider Piper , Lenhard Hayley , Vashisht Apoorva , Ranaldi Robert
Published: November 2022

Background

Reward-related learning, where animals form associations between rewards and stimuli (i.e., conditioned stimuli [CS]) that predict or accompany those rewards, is an essential adaptive function for survival.

Methods

In this study, we investigated the mechanisms underlying the acquisition and performance of conditioned approach learning with a focus on the role of muscarinic acetylcholine (mACh) and NMDA glutamate receptors in the substantia nigra (SN), a brain region implicated in reward and motor processes.

Results

Using RNAscope in situ hybridization assays, we found that dopamine neurons of the SN express muscarinic (mACh5), NMDA2a, NMDA2b, and NMDA2d receptor mRNA but not mACh4. NMDA, but not mACh5, receptor mRNA was also found on SN GABA neurons. In a conditioned approach paradigm, rats were exposed to 3 or 7 conditioning sessions during which light/tone (CS) presentations were paired with delivery of food pellets, followed by a test session with CS-only presentations. Intra-SN microinjections of scopolamine (a mACh receptor antagonist) or AP-5 (a NMDA receptor antagonist) were made either prior to each conditioning session (to test their effects on acquisition) or prior to the CS-only test (to test their effects on expression of the learned response). Scopolamine and AP-5 produced dose-dependent significant reductions in the acquisition, but not performance, of conditioned approach.

Conclusions

These results suggest that SN mACh and NMDA receptors are key players in the acquisition, but not the expression, of reward-related learning. Importantly, these findings redefine the role of the SN, which has traditionally been known for its involvement in motor processes, and suggest that the SN possesses attributes consistent with a function as a hub of integration of primary reward and CS signals.
Modeling the accident prediction for at-grade highway-rail crossings
Authors: Yang Xue , Li Joshua Qiang , Zhang Aonan (Allen) , Zhan You (Jason)
Published: November 2022

Since accidents at highway-rail at-grade crossings (HRGCs) are often catastrophic, safety prediction and evaluation at such locations are of great importance. In this paper, at-grade crossing inventory data and historical accident data were obtained from the Federal Railroad Administration (FRA’s) Office of Safety online databases. The HRGC railroad and highway characteristics were selected as the influencing variables. Considering HRGC accidents are over-dispersed count data with excessive zeros, six count data models, including the Poisson model, negative binomial model (NB), zero-inflated Poisson model (ZIP), zero-inflated negative binomial model (ZINB), hurdle Poisson (HP) model, and hurdle negative binomial model (HNB) were investigated and developed for accident prediction. The ZINB model outperformed the other five models in terms of the goodness-of-fit, zero inflations, and statistical significance of factors. The most significant contributing factors in the ZINB model included the maximum timetabled speed of train, exposure-related variables such as total through trains, highway traffic volume, rural or urban area, and the type of control devices at HRGCs, followed by the minimum speed of train, highway paved or not, and the number of traffic lanes. This study could assist decision-makers with more robust safety evaluation at highway-rail at-grade crossings.
Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep
Authors: Guo Yingwei , Bai Fengting , Wang Jintao , Fu Shaoyin , Zhang Yu , Liu Xiaoyi , Zhang Zhuangbiao , Shao Junjie , Li Ran , Wang Fei , Zhang Lei , Zheng Huiling , Wang Xihong , Liu Yongbin , Jiang Yu
Published: November 2022

The efficiency of molecular breeding largely depends on inexpensive genotyping arrays. In this study, we aimed to develop an ovine high-resolution multiple-single-nucleotide polymorphism (SNP) capture array, based on genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology. All the markers were from 40K captured regions, including genes located within selective sweep regions, breed-specific regions, quantitative trait loci (QTL), and the potential functional SNPs on the sheep genome. The results showed that a total of 210K high-quality SNPs were identified in the 40K regions, indicating a high average capture ratio (99.7%) for the target genomic regions. Using genotyped data (n = 317) from liquid chip technology, we further performed genome-wide association studies (GWAS) to detect the genetic loci affecting sheep hair types and teat number. A single signiﬁcant association signal for hair types was identified on 6.7-7.1 Mb of chromosome 25. The IRF2BP2 gene (chr25: 7,067,974-7,071,785), which is located within this genomic region, has been previously known to be involved in hair/wool traits in sheep. The results further showed a new candidate region around 26.4 Mb of chromosome 13, between the ARHGAP21 and KIAA1217 genes, that was significantly related to teat number in sheep. The haplotype patterns of this region also showed differences in animals with 2, 3, or 4 teats. Advances in using the high-accuracy and low-cost liquid chip are expected to accelerate sheep genomic and breeding studies in the coming years.
Serum metabolomic characterization in pigs in relation to birth weight category and neonatal nutrition
Authors: Wellington Michael O , Rodrigues Lucas A , Quinn Melissa A , Panisson Josiane C , Ferguson David P , Columbus Daniel A
Published: November 2022

The objective of this study was to characterize developmental differences in low birth weight (LBW) and normal birth weight (NBW) piglets with or without pre-weaning nutrient restriction using serum metabolomic profile analysis. At farrowing, 112 piglets were identified as LBW (1.22 ± 0.28 kg) or NBW (1.70 ± 0.27 kg) and were randomly assigned to receive normal nutrition (NN) or restricted nutrition (RN) (6 h/day no suckling) from days 2 to 28 post farrow (n = 8 pigs/group). On day 28, piglets were weaned onto a common diet. Fasted blood samples were obtained on days 28 and 56 (n = 8 pigs/group) and were analyzed using quantitative metabolomics via a combination of direct injection mass spectrometry with a reverse-phase LC–MS/MS custom assay. Data were normalized using logarithmic transformation and auto-scaling. Partial least squares discriminant analysis (PLS-DA) was carried out to further explore the differential metabolites among the groups (metaboanalyst.ca) with an integrated enrichment and pathway topography analysis. On day 28, LBW piglets had lower levels of essential amino acids as well as reduced metabolites associated with fatty acid oxidation, glycolysis, and the tri-carboxylic acid (TCA) cycle compared to the NBW group. The overall reduction of metabolites associated with energy production and regulation suggests that LBW vs. NBW are in an energy-survival state. On day 56, LBW pigs had increased utilization of fatty acids and resultant ketone production, evident by increased carnitines, acetoacetate, β-hydroxybutyrate, and glycerol compared to NBW pigs. In addition, compared to the NBW pigs LBW pigs had a consistent decrease in serum glucose and lactate as well as reduced TCA cycle metabolites: pyruvate, succinate, citrate, and α-ketoglutaric acid similar to day 28. Low reliance on glycolysis and the TCA cycle and higher glycerol production in the LBW pigs may indicate impairments in glucose tolerance at 56 d. In summary, LBW piglets appear to have more metabolic alterations in early life, which is not resolved with adequate nutrition or refeeding and may elucidate physiological and metabolic mechanisms of poor growth and life performance compared to NBW pigs later in life.
Qi Wei Anti-burn Tincture Remodels Liver Metabolic Pathways and Treats Burn Wounds Efficiently
Authors: Wang Shuai , Zhou Hui , Cui Weiqi , Zhang Junwei , Wu Deqiao , Zhang Nan , Xu Xia
Published: November 2022

This work aims to elucidate the molecular mechanism of Qi Wei anti-burn Tincture (QW) on wound healing in burnt mice using metabolomics and molecular biology techniques. A scald model was first established in Kunming mice. After treatment, biochemical indicators for liver function and burnt skin tissues were then evaluated via biochemical detection and HE staining, respectively. Liver tissues were further analyzed for differential metabolites, inflammatory factors, and mRNA levels of cytokines using metabolomics and molecular biology techniques. Involved metabolic pathways were also identified using software. QW treatment did promote the healing of the burn wounds in Kunming mice with a downregulation of ALP, ALT, and AST to normal levels. In mouse liver tissue, the contents of glutamine, aspartic acid, and citrulline were significantly reduced, while the contents of 5-hydroxyproline, taurine, hypotaurine, and glutamic acid significantly increased. These major differential compounds are involved in the arginine metabolic pathway, nitrogen excretion, and the metabolism of taurine and hypotaurine, suggesting that QW reprogramed the above metabolic processes in the liver. Furthermore, the application of QW increased the expression of TGF-β1 and FGF-2 and reduced the levels of TNF-α, IL-1β, IL-6, and reactive oxygen species in the liver of mice induced by burn injury. This study found that QW treatment promoted metabolic pathway remodeling in the liver, which might be a potential mechanism for QW to treat burn wounds.
Two Cases of COVID-19 Patients With Associated Purpura Fulminans
Authors: Pangburn Jane , Gibbs Jeffrey
Published: November 2022

Purpura fulminans (PF) is a life-threatening emergency involving coagulopathy and widespread skin necrosis. Early treatment, especially surgical management, is imperative as prognosis can be very poor. PF is most commonly associated with severe bacterial illness; however, viral causes are also possible. Currently in the literature, there have only been a handful of PF cases associated with COVID-19. We present two cases of PF in the setting of COVID-19 infection. Both patients had a history of underlying coagulopathies. PF can be a sign of underlying coagulopathy in a COVID-19 patient, who is already at increased risk for thromboembolic events due to the inflammatory nature of COVID itself. Due to how quickly PF can develop into life-threatening necrosis and multiorgan failure, it is imperative that these patients are referred early to a burn center for more advanced care.
Comparison of dosimetries of carbon-ion pencil beam scanning, proton pencil beam scanning and volumetric modulated arc therapy for locally recurrent rectal cancer
Authors: Mori Shinichiro , Bhattacharyya Tapesh , Furuichi Wataru , Tohyama Naoki , Nomoto Akihiro , Shinoto Makoto , Takiyama Hirotoshi , Yamada Shigeru
Published: November 2022

We compared the dose distributions of carbon-ion pencil beam scanning (C-PBS), proton pencil beam scanning (P-PBS) and Volumetric Modulated Arc Therapy (VMAT) for locally recurrent rectal cancer.

The C-PBS treatment planning computed tomography (CT) data sets of 10 locally recurrent rectal cancer cases were randomly selected. Three treatment plans were created using identical prescribed doses. The beam angles for C-PBS and P-PBS were identical. Dosimetry, including the dose received by 95% of the planning target volume (PTV) (D95%), dose to the 2 cc receiving the maximum dose (D2cc), organ at risk (OAR) volume receiving > 15Gy (V15) and > 30Gy (V30), was evaluated. Statistical significance was assessed using the Wilcoxon signed-rank test. Mean PTV-D95% values were > 95% of the volume for P-PBS and C-PBS, whereas that for VMAT was 94.3%. However, PTV-D95% values in P-PBS and VMAT were < 95% in five and two cases, respectively, due to the OAR dose reduction. V30 and V15 to the rectum/intestine for C-PBS (V30 = 4.2 ± 3.2 cc, V15 = 13.8 ± 10.6 cc) and P-PBS (V30 = 7.3 ± 5.6 cc, V15 = 21.3 ± 13.5 cc) were significantly lower than those for VMAT (V30 = 17.1 ± 10.6 cc, V15 = 55.2 ± 28.6 cc). Bladder-V30 values with P-PBS/C-PBS (3.9 ± 4.8 Gy(RBE)/3.0 ± 4.0 Gy(RBE)) were significantly lower than those with VMAT (7.9 ± 8.1 Gy). C-PBS provided superior dose conformation and lower OAR doses compared with P-PBS and VMAT. C-PBS may be the best choice for cases in which VMAT and P-PBS cannot satisfy dose constraints. C-PBS could be another choice for cases in which VMAT and P-PBS cannot satisfy dose constraints, thereby avoiding surgical resection.
Sarcomatoid mesothelioma: unusual findings and literature review
Authors: Clopton Brittni , Long Winnie , Santos Monica , Asarian Armand , Genato Romulo , Xiao Philip
Published: November 2022

Sarcomatoid mesothelioma is an aggressive disease secondary to its propensity to undergo rapid growth, show inconsistent expression of tumor markers and invade surrounding tissues. Therefore, there are numerous obstacles that clinical researchers face as they look for new methods to diagnose and treat the malignancy. We present a case of sarcomatoid mesothelioma, originally thought to be metastasis from renal cell carcinoma.
Combined pantaloon and femoral hernia: a common pathology in medicine occurring simultaneously
Authors: Rajkumar Karnan , Trivedi Aakash , Molavi Ida , Talishinskiy Toghrul
Published: November 2022

Inguinal hernias are typically classified based on their location and can be divided into two types. The most commonly seen inguinal hernias are direct and indirect, which can both potentially require surgical intervention. When both types of hernias are seen simultaneously, it is classified as a pantaloon hernia. This case describes an instance of a femoral hernia being found along with a pantaloon hernia. We present a case of what was projected to be a common inguinal hernia repair but progressed to a rare presentation of a femoral hernia superimposed on a pantaloon hernia. Pantaloon hernias plus a femoral hernia is a rare defect that does not present as often as the different types of isolated hernias.
Late presentation of midgut malrotation in a young adult
Authors: Lodhia Jay , Salewi Anande Kumbwaeli , Sway Happiness , Sadiq Adnan , Msuya David
Published: November 2022

Midgut malrotation is a congenital anomaly due to partial or complete failure of rotation of the midgut in fetal life. Majority of the cases present in the neonatal period and 90% within the first year. Adult presentation is rare and the true incidence is unknown as some cases pass undiagnosed. Whirlpool sign is pathognomic for midgut malrotation and management involves surgery.
Unroofing osteotomy for dissociated tibial intramedullary magnetic rod during implant removal: a case report
Authors: Dharamsi Miraal , Castagno Christopher , Klahs Kyle J , Abdelgawad Amr , Thabet Ahmed M
Published: November 2022

The PRECICE® intramedullary rod (NuVasive, San Diego, CA) utilizes multiple telescopic components to magnetically drive limb lengthening. These devices are routinely explanted after desired growth correction is met. To the author’s knowledge, this is the first description of an osteotomy assisted extraction of a disassociated tibial magnetic lengthening rod. A 17-year-old girl with fibular hemimelia and resolved left tibial length discrepancy after successful surgical lengthening underwent a complex implant removal approximately seven years after regenerate consolidation. During implant removal, the telescopic portion of the rod remained lodged in the tibial medullary canal and a subsequent unroofing osteotomy of the tibia was performed. Tibial limb length discrepancies are oftentimes corrected with complex implants comprised of multiple fragile components that are routinely explanted. During the unfortunate event of a telescopic intramedullary rod dissociation, an unroofing osteotomy can be successfully performed to removal all implant components.
Fibrous dysplasia of the sphenoid sinus: headache relieved by surgical excision—a case report
Authors: Jawad Jamal , Al-Domaidat Derar , Abaza Mohamed
Published: November 2022

Fibrous dysplasia (FD) is an uncommon benign bone disorder of unknown etiology in which normal medullary bone is replaced by fibrotic and osseous tissue. FD of paranasal sinuses is usually secondary to extension from adjacent bones. It is rarely limited to the sinuses, let alone limited to the sphenoid sinus. Furthermore, the relationship between headache and FD of paranasal sinuses has not been well addressed. We report a case of a 55-year-old female with FD of sphenoid sinuses complaining of sever right-sided parietal headache. Her headache was significantly improved after surgical excision of FD.
A case of anterior choroidal artery injury after resection of a pilocytic astrocytoma in the amygdale—a case report
Authors: Moustafa Wahab , Karamani Lydia , Schreiber Stefan
Published: November 2022

The anterior choroidal artery (AChA) arises from the last segment of internal carotid artery (ACI), the communicating C7 segment and comprises the terminal branch of ACI. Anatomical its origin located supraclionoidal after the ophthalmic C6 segment of ACI and after the rise of posterior communicating artery. The AChA gains greater importance because of its small size and its region of blood supply. With its perforating branches supplies important intracranial structures such as the optic tract, the posterior limb of the internal capsule, the lateral geniculate body, the medial temporal lobe and the medial area of the pallidum. The anterior choroidal artery is a fine artery and consists of two parts, a cisternal and a plexal one. There are only few studies published, which describe the exact anatomy and the impact of its damage. On the present report, we discuss a case of an iatrogenic injury of the anterior choroidal artery and its hazardous consequences.
Cholecystocolonic fistula: two different presentations of this rare complication of gallstones
Authors: Salas-Parra Ruben D , Hattingh Genevieve , Shumway Karlie R , Esposito Kathryn , Lois William , Farkas Daniel T
Published: November 2022

Cholecystocolonic fistulas (CCF) are a rare but significant complication of biliary disease, frequently presenting as gallstone ileus. Although there is no one agreed-upon procedure, enterolithotomy appears to be the initial treatment of choice; with a subsequent cholecystectomy performed ~4–8 weeks later. Alternatively, a patient may undergo a single-stage procedure, at which time an enterolithotomy, cholecystectomy and fistula closure are performed. Herein, we describe two patients with chronic cholecystitis and subsequent development of CCF with differing presentations. We report the clinical, radiographic and intraoperative findings and discuss the surgical treatment options for each patient, respectively.
A successful management of left-sided posterior congenital diaphragmatic hernia of the jejunum, ileum, colon and left kidney: a case report
Authors: Al-Abdullah Zainab , Duvuru Ruthwik , Nawaz Faisal A , Ennab Farah , Alklani Temaa , Ahmed Aftab
Published: November 2022

Congenital diaphragmatic hernia (CDH) is a rare developmental anomaly in which abdominal contents herniate into the thoracic cavity due to underdevelopment of the diaphragm, possibly leading to pulmonary hypoplasia. Whereas surgery is not the first priority in treatment, it must be performed within a window of 2 weeks and after hemodynamic stability has been achieved. The patient described in this case report had a CDH of the jejunum, ileum, colon and left kidney diagnosed in a boy of South Asian origin who presented with tachypnea in the third hour of life. Imaging studies conducted included chest X-ray, chest ultrasound including echocardiogram, and abdominal and pelvic ultrasound. Treatment and management were successful despite complications. Future research on CDH is warranted in the populations in the Middle East, and local guidelines must be generated in order to improve diagnosis, treatment and prognosis.
The transcription factor OsWRKY10 inhibits phosphate uptake via suppressingOsPHT1;2expression under phosphate-replete conditions in rice
Authors: Wang Shichao , Xu Tingting , Chen Min , Geng Liyan , Huang Zhaoyang , Dai Xiaoli , Qu Hongye , Zhang Jun , Li Huanhuan , Gu Mian , Xu Guohua
Published: November 2022

Plants have evolved delicate systems for stimulating or inhibiting inorganic phosphate (Pi) uptake in response to the fluctuating Pi availability in soil. However, the negative regulators inhibiting Pi uptake at the transcriptional level are largely unexplored. Here, we functionally characterized a transcription factor in rice (Oryza sativa), OsWRKY10. OsWRKY10 encodes a nucleus-localized protein and showed preferential tissue localization. Knockout of OsWRKY10 led to increased Pi uptake and accumulation under Pi-replete conditions. In accordance with this phenotype, OsWRKY10 was transcriptionally induced by Pi, and a subset of PHOSPHATE TRANSPORTER 1 (PHT1) genes were up-regulated upon its mutation, suggesting that OsWRKY10 is a transcriptional repressor of Pi uptake. Moreover, rice plants expressing the OsWRKY10–VP16 fusion protein (a dominant transcriptional activator) accumulated even more Pi than oswrky10. Several lines of biochemical evidence demonstrated that OsWRKY10 directly suppressed OsPHT1;2 expression. Genetic analysis showed that OsPHT1;2 was responsible for the increased Pi accumulation in oswrky10. Furthermore, during Pi starvation, OsWRKY10 protein was degraded through the 26S proteasome. Altogether, the OsWRKY10–OsPHT1;2 module represents a crucial loop in the Pi signaling network in rice, inhibiting Pi uptake when there is ample Pi in the environment.
Rubisco, the imperfect winner: it’s all about the base
Authors: Badger Murray R , Sharwood Robert E
Published: November 2022

Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles’ heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth’s multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco’s catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.
Investigating the shift between externally and internally oriented cognition: a novel task-switching paradigm
Authors: Calzolari Sara , Boneva Svetla , Fernández-Espejo Davinia
Published: November 2022

Despite our constant need to flexibly balance internal and external information, research on cognitive flexibility has focused solely on shifts between externally oriented tasks. In contrast, switches across internally oriented processes (and self-referential cognition specifically) and between internal and external domains have never been investigated. Here, we report a novel task-switching paradigm developed to explore the behavioural signatures associated with cognitive flexibility when self-referential processes, as well as more traditional external processes, are involved. Two hundred healthy volunteers completed an online task. In each trial, participants performed one of four possible tasks on written words, as instructed by a pre-stimulus cue. These included two externally and two internally oriented tasks: assessing whether the third letter was a consonant or the penultimate letter was a vowel versus assessing whether the adjective applied to their personality or if it described a bodily sensation they were currently experiencing. In total, 40% of trials involved switches to another task, and these were equally distributed across within-external, within-internal, internal-to-external and external-to-internal switches. We found higher response times for switches compared to repetitions both in the external and internal domains, thus demonstrating the presence of switch costs in self-referential tasks for the first time. We also found higher response times for between-domain switches compared to switches within each domain. We propose that these effects originate from the goal-directed engagement of different domain-specific cognitive systems that flexibly communicate and share domain-general control features.
Phase I study of a novel glioblastoma radiation therapy schedule exploiting cell-state plasticity
Authors: Dean Jamie A , Tanguturi Shyam K , Cagney Daniel , Shin Kee-Young , Youssef Gilbert , Aizer Ayal , Rahman Rifaquat , Hammoudeh Lubna , Reardon David , Lee Eudocia , Dietrich Jorg , Tamura Kaoru , Aoyagi Masaru , Wickersham Lacey , Wen Patrick Y , Catalano Paul , Haas-Kogan Daphne , Alexander Brian M , Michor Franziska
Published: November 2022

Background

Glioblastomas comprise heterogeneous cell populations with dynamic, bidirectional plasticity between treatment-resistant stem-like and treatment-sensitive differentiated states, with treatment influencing this process. However, current treatment protocols do not account for this plasticity. Previously, we generated a mathematical model based on preclinical experiments to describe this process and optimize a radiation therapy fractionation schedule that substantially increased survival relative to standard fractionation in a murine glioblastoma model.

Methods

We developed statistical models to predict the survival benefit of interventions to glioblastoma patients based on the corresponding survival benefit in the mouse model used in our preclinical study. We applied our mathematical model of glioblastoma radiation response to optimize a radiation therapy fractionation schedule for patients undergoing re-irradiation for glioblastoma and developed a first-in-human trial (NCT03557372) to assess the feasibility and safety of administering our schedule.

Results

Our statistical modeling predicted that the hazard ratio when comparing our novel radiation schedule with a standard schedule would be 0.74. Our mathematical modeling suggested that a practical, near-optimal schedule for re-irradiation of recurrent glioblastoma patients was 3.96 Gy × 7 (1 fraction/day) followed by 1.0 Gy × 9 (3 fractions/day). Our optimized schedule was successfully administered to 14/14 (100%) patients.

Conclusions

A novel radiation therapy schedule based on mathematical modeling of cell-state plasticity is feasible and safe to administer to glioblastoma patients.
Upfront BRAF/MEK inhibitors for treatment of high-grade glioma: A case report and review of the literature
Authors: Arbour Gabrielle , Ellezam Benjamin , Weil Alexander G , Cayrol Romain , Vanan Magimairajan Issai , Coltin Hallie , Larouche Valérie , Erker Craig , Jabado Nada , Perreault Sébastien
Published: November 2022

Background

High-grade gliomas (HGG) with BRAFV600E mutation represent a unique subset of central nervous system tumors. Targeted therapies including BRAF and MEK inhibitors are now being explored as possible new treatment options.

Methods

We report an 18-year-old female with a grade 3 pleomorphic xanthoastrocytoma treated upfront with dabrafenib and trametinib. We also conducted a systematic literature review of patients with HGG and BRAFV600E mutations treated with BRAF inhibitors.

Results

Despite local recurrences resected surgically, the patient has been on dabrafenib and trametinib for more than 54 months. Thirty-two patients with HGG and BRAFV600E mutations treated with BRAF inhibitors were retrieved through our systematic review of the literature. Only 1 young patient with an anaplastic ganglioglioma was treated upfront with a BRAF inhibitor with a curative intent. Best response reported with radiation therapy and systemic therapy was a stable disease (SD) for 18 patients (56.3%) and progressive disease (PD) for 9 patients (28.1%). Responses to treatment regimens that included BRAF inhibitors were reported in 31 patients and included 4 complete responses (12.9%), 23 partial responses (74.2%), 2 SDs (6.5%), and 2 PDs (6.5%).

Conclusions

Our patient had durable disease control with dabrafenib and trametinib. Given favorable responses reported in patients with HGG treated with BRAF inhibitors, we believe that upfront targeted therapy is a possible treatment approach that should be studied in the context of a clinical trial.