bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wide-field endoscope accessory for multiplexed fluorescence imaging
Authors: Li Gaoming , Lee Miki , Chang Tse-Shao , Yu Joonyoung , Li Haijun , Duan Xiyu , Wu Xiaoli , Jaiswal Sangeeta , Feng Shuo , Oldham Kenn R. , Wang Thomas D. 
Published: November 2023

AbstractA wide-field endoscope that is sensitive to fluorescence can be used as an adjunct to conventional white light endoscopy by detecting multiple molecular targets concurrently. We aim to demonstrate a flexible fiber-coupled accessory that can pass forward through the instrument channel of standard medical endoscopes for clinical use to collect fluorescence images. A miniature scan mirror with reflector dimensions of 1.30 × 0.45 mm2was designed, fabricated, and placed distal to collimated excitation beams at λex = 488, 660, and 785 nm. The mirror was driven at resonance for wide angular deflections in the X and Y-axes. A large image field-of-view (FOV) was generated in real time. The optomechanical components were packaged in a rigid distal tip with dimensions of 2.6 mm diameter and 12 mm length. The scan mirror was driven at 27.6 and 9.04 kHz in the fast (X) and slow (Y) axes, respectively, using a square wave with 50% duty cycle at 60 Vppto collect fluorescence images at 10 frames per sec. Maximum total divergence angles of ± 27.4° and ± 22.8° were generated to achieve a FOV of 10.4 and 8.4 mm, respectively, at a working distance of 10 mm. Multiplexed fluorescence images were collected in vivo from the rectum of live mice using 3 fluorescently-labeled peptides that bind to unique cell surface targets. The fluorescence images collected were separated into 3 channels. Target-to-background ratios of 2.6, 3.1, and 3.9 were measured. This instrument demonstrates potential for broad clinical use to detect heterogeneous diseases in hollow organs.
An expandable voice user interface as lab assistant based on an improved version of Google’s speech recognition
Authors: Avila Vazquez Maria Fernanda , Rupp Nicole , Ballardt Larissa , Opara Jeannine , Zuchner Thole 
Published: November 2023

AbstractVoice assistants are potentially helpful when working in a scientific laboratory. A big challenge is the extremely specific use of language in every laboratory. As with any voice assistant, another concern is data security. Here, we present Rainbow—an open source voice user interface (VUI) for scientific laboratories, that is adaptable to any Windows PC with Internet access. We used Google Translate Site (GTS) as a voice input and output system to ensure communication to the user. The scripting language AutoIt controls GTS, executes all actions and builds the VUI. Rainbow performs tasks from three different areas—general Microsoft Windows tasks, lab-specific tasks, and device-specific tasks. We achieved significantly higher speech recognition accuracy with our VUI than with GTS alone (91.3% versus 85.1%). Because of Rainbow's architecture, it is possible to improve the voice assistant in terms of functionality and accuracy, allowing each laboratory to optimize its own Rainbow system in a user-friendly way. In a test setup, this led to a speech recognition accuracy of 98.6%. Taken together, Rainbow provides an opportunity for every scientist to implement highly specific scientific terms and tasks to this open source voice assistant system in a very user-friendly way.
Research on image recognition of three Fritillaria cirrhosa species based on deep learning
Authors: Chen Yuxiu , Li Yuyan , Zhang Sheng 
Published: November 2023

AbstractBased on the deep learning method, a network model that can quickly and accurately identify the species ofFritillaria cirrhosaspecies was constructed. The learning method based on deep residual convolutional neural network was used to input the unprocessed original image directly as input, and the features of the image were extracted through convolution and pooling operations. On this basis, the ResNet34 model was improved, and the additional fully connected layer was added in front of the Softmax classifier to improve the learning ability of the network model. Total of 3915 images of three kinds ofFritillaria cirrhosawere used as data sources for the experiments, among which 160 images of each type were randomly selected to form the validation set. The final training set recognition accuracy rate was 95.8%, the validation set accuracy rate reached 92.3%, and the test set accuracy rate was 88.7%. The image recognition method ofFritillaria cirrhosabased on deep learning proposed in this paper is effective and feasible, which can quickly and accurately identify the species ofFritillaria cirrhosaspecies, and provides a new idea for the intelligent recognition of Chinese medicinal materials.
Dysfunctional TLR1 reduces the therapeutic efficacy of chemotherapy by attenuating HMGB1-mediated antitumor immunity in locally advanced colorectal cancer
Authors: Huang Kevin Chih-Yang , Ke Tao-Wei , Chen Jia-Yi , Hong Wei-Ze , Chiang Shu-Fen , Lai Chia-Ying , Chen Tsung-Wei , Yang Pei-Chen , Chen Liang-Chi , Liang Ji-An , Chen William Tzu-Liang , Chao K. S. Clifford 
Published: November 2023

AbstractRegional lymph node metastasis is an important predictor for survival outcome and an indicator for postoperative adjuvant chemotherapy in patients with colorectal cancer. Even with advances in adjuvant chemotherapeutic regimens, 5-year distant metastasis and survival rates are still unsatisfactory. Here, we evaluate the clinical significance of polymorphisms in receptors for HMGB1, which is the hallmark of chemotherapy-induced immunogenic cell death, in patients with stage II–III colon carcinoma (COAD). We found that high cytosolic HMGB1 is elicited in stage III COAD patients who received adjuvant chemotherapy. Patients with the TLR1-N248S polymorphism (rs4833095), which causes loss-of-function in HMGB1-mediated TLR1–TLR2 signaling, may influence the therapeutic efficacy of adjuvant chemotherapy, leading to a high risk of distant metastasis within 5 years [HR = 1.694, 95% CI = 1.063–2.698, p = 0.027], suggesting that TLR1-N248S is an independent prognostic factor for locally advanced colon carcinoma patients. We found that defective TLR1 impaired TLR1/2 signaling during dendritic cell (DC) maturation for the antitumor immune response under immunogenic chemotherapy oxaliplatin (OXP) treatment. Defective TLR1 on DCs impaired their maturation ability by HMGB1 and reduced the secretion of IFNγ from T cells to eradicate tumor cells in vitro. Moreover, systemic inhibition of TLR1/2 dramatically reduced the tumor-infiltrating immune cells by OXP treatment, leading to poor therapeutic response to OXP. In contrast, administration of a TLR1/2 agonist synergistically increased the benefit of OXP treatment and triggered a high density of tumor-infiltrating immune cells. We also observed that fewer tumor-infiltrating cytotoxic T lymphocytes were located within the tumor microenvironment in patients bearing the TLR1-N248S polymorphism. Overall, our results suggest that dysfunctional TLR1 may reduce the therapeutic response to adjuvant chemotherapy by impairing HMGB1-mediated DC maturation and attenuating the antitumor immune response in locally advanced colon carcinoma patients.
Changes in peripapillary microvasculature in patients with type 2 diabetes patients: effect of systemic hypertension
Authors: Sung Jae-Yun , Lee Kook-Hyung , Jun Ji-Ho , Lee Min-Woo 
Published: November 2023

AbstractTo determine the effect of hypertension (HTN) on the peripapillary microvasculature in type 2 diabetes mellitus (T2DM) patients without diabetic retinopathy (DR). The patients were classified into three groups: the control group (group 1), T2DM group (group 2), and both T2DM and HTN group (group 3). Peripapillary vessel density (VD) was compared using analysis of covariance and linear regression analysis was performed to identify the factors affecting the peripapillary VD. A total of 286 eyes were enrolled: 124 in group 1, 111 in group 2, and 51 in group 3. The peripapillary VDs for the full area were 18.3 ± 0.6, 17.8 ± 1.0, and 17.3 ± 1.2 mm−1 in group 1, group 2, and group 3, respectively, which were significantly different after adjustment for age and best-corrected visual acuity (P < 0.001). In post hoc analyses, group 1 versus group 2 (P < 0.001), group 1 versus group 3 (P < 0.001), and group 2 versus group 3 (P = 0.001) showed significant differences. In linear regression analysis, HTN (B =  − 0.352, P = 0.043) and peripapillary retinal nerve fiber layer (pRNFL) thickness (B = 0.045, P < 0.001) were significantly associated with peripapillary VD in T2DM patients. Peripapillary VD in T2DM patients without clinical DR were lower compared to normal controls, and they were more decreased when HTN was comorbid. The combination of ischemic damage by high blood pressure and impairment of the neurovascular unit by hyperglycemia would result in more severe deterioration of peripapillary microvasculature, and this impairment could be also reflected by pRNFL thinning.
The metabolic effects of intermittent versus continuous feeding in critically ill patients
Authors: Wilkinson D. , Gallagher I. J. , McNelly A. , Bear D. E. , Hart N. , Montgomery H. E. , Le Guennec A. , Conte M. R. , Francis T. , Harridge S. D. R. , Atherton P. J. , Puthucheary Z. A. 
Published: November 2023

AbstractIntermittent (or bolus) feeding regimens in critically ill patients have been of increasing interest to clinicians and scientists. Changes in amino acid, fat and carbohydrate metabolites over time might yet deliver other benefits (e.g. modulation of the circadian rhythm and sleep, and impacts on ghrelin secretion, insulin resistance and autophagy). We set out to characterise these changes in metabolite concentration. The Intermittent versus Continuous Feeding in Critically Ill paitents study (NCT02358512) was an eight-centre single-blinded randomised controlled trial. Patients were randomised to received a continuous (control arm) or intermittent (6x/day, intervention arm) enteral feeding regimen. Blood samples were taken on trial days 1, 7 and 10 immediately before and 30 min after intermittent feeds, and at equivalent timepoints in the control arm. A pre-planned targeted metabolomic analysis was performend using Nuclear Resonance Spectroscopy. Five hundred and ninety four samples were analysed from 75 patients. A total of 24 amino acid-, 19 lipid based-, and 44 small molecule metabolite features. Across the main two axes of variation (40–60% and 6–8% of variance), no broad patterns distinguished between intermittent or continuous feeding arms, across intra-day sampling times or over the 10 days from initial ICU admission. Logfold decreases in abundance were seen in metabolites related to amino acids (Glutamine − 0.682; Alanine − 0.594), ketone body metabolism (Acetone − 0.64; 3-Hydroxybutyric Acid − 0.632; Acetonacetic Acid − 0.586), fatty acid (carnitine − 0.509) and carbohydrate metabolism ( Maltose − 0.510; Citric Acid − 0.485). 2–3 Butanediol, a by-product of sugar-fermenting microbial metabolism also decreased (− 0.489). No correlation was seen with change in quadriceps muscle mass for any of the 20 metabolites varying with time (all p > 0.05). Increasing severity of organ failure was related to increasing ketone body metabolism (3 Hydroxybutyric Acid-1 and − 3; p = 0.056 and p = 0.014), carnitine deficiency (p = 0.002) and alanine abundancy (p − 0.005). A 6-times a day intermittent feeding regimen did not alter metabolite patterns across time compared to continuous feeding in critically ill patients, either within a 24 h period or across 10 days of intervention. Future research on intermittent feeding regimens should focus on clinical process benefits, or extended gut rest and fasting.
Histological classification of canine and feline lymphoma using a modular approach based on deep learning and advanced image processing
Authors: Haghofer Andreas , Fuchs-Baumgartinger Andrea , Lipnik Karoline , Klopfleisch Robert , Aubreville Marc , Scharinger Josef , Weissenböck Herbert , Winkler Stephan M. , Bertram Christof A. 
Published: November 2023

AbstractHistopathological examination of tissue samples is essential for identifying tumor malignancy and the diagnosis of different types of tumor. In the case of lymphoma classification, nuclear size of the neoplastic lymphocytes is one of the key features to differentiate the different subtypes. Based on the combination of artificial intelligence and advanced image processing, we provide a workflow for the classification of lymphoma with regards to their nuclear size (small, intermediate, and large). As the baseline for our workflow testing, we use a Unet++ model trained on histological images of canine lymphoma with individually labeled nuclei. As an alternative to the Unet++, we also used a publicly available pre-trained and unmodified instance segmentation model called Stardist to demonstrate that our modular classification workflow can be combined with different types of segmentation models if they can provide proper nuclei segmentation. Subsequent to nuclear segmentation, we optimize algorithmic parameters for accurate classification of nuclear size using a newly derived reference size and final image classification based on a pathologists-derived ground truth. Our image classification module achieves a classification accuracy of up to 92% on canine lymphoma data. Compared to the accuracy ranging from 66.67 to 84% achieved using measurements provided by three individual pathologists, our algorithm provides a higher accuracy level and reproducible results. Our workflow also demonstrates a high transferability to feline lymphoma, as shown by its accuracy of up to 84.21%, even though our workflow was not optimized for feline lymphoma images. By determining the nuclear size distribution in tumor areas, our workflow can assist pathologists in subtyping lymphoma based on the nuclei size and potentially improve reproducibility. Our proposed approach is modular and comprehensible, thus allowing adaptation for specific tasks and increasing the users’ trust in computer-assisted image classification.
Assessing the efficacy of jet dispenser versus direct syringe injection for calcium hydroxide paste placement in artificial root canals
Authors: Song Youngwook , Ham Hwichan , Lee WooCheol , Kim Ryan Jin Young 
Published: November 2023

AbstractThis study aimed to evaluate the efficacy of a novel jet dispenser (JD) for filling simulated straight and curved canals with calcium hydroxide (Ca(OH)2) paste by comparing the level of intracanal medicament with traditional direct syringe delivery. The Ca(OH)2 paste was delivered into the canals using either a direct syringe with binding tip and unbinding tip or a JD. The analysis of the ratio of the canal filled area (RCFA) in the coronal, middle, and apical thirds was conducted using the Kruskal–Wallis and Mann–Whitney U tests (α = 0.05). The JD resulted in a significantly higher RCFA of 1.00 in the middle and apical thirds in both the straight and curved canals than the direct syringe method (p < 0.001). Voids were frequently observed in the direct syringe group, whereas JD showed no voids within the filled area. In the direct syringe groups, the apical area was more readily filled in both canal types when the tip was bound (p < 0.001). The JD was found to be more effective in filling the entire canal space than the binding and unbinding conditions of the direct injection method, particularly in the apical area.
Performance of standardized cancer patient pathways in Sweden visualized using observational data and a state-transition model
Authors: Borg Sixten , Hörstedt Ann-Sofi , Carlsson Tobias , Nilbert Mef , Larsson Anna-Maria , Ohlsson Björn 
Published: November 2023

AbstractStandardized Cancer Patient Pathways (CPPs) were introduced in Swedish healthcare starting in 2015 to improve diagnostics for patients with symptoms of cancer, patient satisfaction and equity of care between healthcare providers. An inclusion target and a time target were set. Our primary aim was to visualize the patient population going through CPPs, in terms of investigation time and indications of the various outcomes including cancer diagnoses. Our secondary aims were to examine if targets were met, and to examine frequencies of undetected cancer. We collected data from 19,204 patients starting in a CPP, and 7895 patients diagnosed with cancer in 2018 in a region of Sweden. A state transition model was developed and used as analytical framework, and patients were mapped over time in the states of the model. Visualization of the patient-flow through the model illustrates speed of investigation, time to treatment, frequencies of detected and undetected cancer. Twelve CPPs out of 28 met the inclusion target, five met the time target. After suspicion of cancer rejected, 0.8% of patients were diagnosed with the primarily suspected cancer, 1.0% with another cancer. In patients not meeting the criteria for well-founded suspicion less than 3% were later diagnosed with cancer. The visualization of the patient flow into and through standardized cancer patient pathways illustrates investigation time, events occurring and outcomes. The use of standardized cancer patient pathways detects cancer efficiently.
Erythropoietin regulates developmental myelination in the brain stimulating postnatal oligodendrocyte maturation
Authors: Muttathukunnel Paola , Wälti Michael , Aboouf Mostafa A. , Köster-Hegmann Christina , Haenggi Tatjana , Gassmann Max , Pannzanelli Patrizia , Fritschy Jean-Marc , Schneider Gasser Edith M. 
Published: November 2023

AbstractMyelination is a process tightly regulated by a variety of neurotrophic factors. Here, we show—by analyzing two transgenic mouse lines, one overexpressing EPO selectively in the brain Tg21(PDGFB-rhEPO) and another with targeted removal of EPO receptors (EPORs) from oligodendrocyte progenitor cells (OPC)s (Sox10-cre;EpoRfx/fx mice)—a key function for EPO in regulating developmental brain myelination. Overexpression of EPO resulted in faster postnatal brain growth and myelination, an increased number of myelinating oligodendrocytes, faster axonal myelin ensheathment, and improved motor coordination. Conversely, targeted ablation of EPORs from OPCs reduced the number of mature oligodendrocytes and impaired motor coordination during the second postnatal week. Furthermore, we found that EPORs are transiently expressed in the subventricular zone (SVZ) during the second postnatal week and EPO increases the postnatal expression of essential oligodendrocyte pro-differentiation and pro-maturation (Nkx6.2 and Myrf) transcripts, and the Nfatc2/calcineurin pathway. In contrast, ablation of EPORs from OPCs inactivated the Erk1/2 pathway and reduced the postnatal expression of the transcripts. Our results reveal developmental time windows in which EPO therapies could be highly effective for stimulating oligodendrocyte maturation and myelination.
Accurate emulation of steady-state and dynamic performances of PEM fuel cells using simplified models
Authors: Ashraf Hossam , Elkholy Mahmoud M. , Abdellatif Sameh O. , El‑Fergany Attia A. 
Published: November 2023

AbstractThe current effort addresses a novel attempt to extract the seven ungiven parameters of PEMFCs stack. The sum of squared deviations (SSDs) among the measured and the relevant model-based calculated datasets is adopted to define the cost function. A Kepler Optimization Algorithm (KOA) is employed to decide the best values of these parameters within viable ranges. Initially, the KOA-based methodology is applied to assess the steady-state performance for four practical study cases under several operating conditions. The results of the KOA are appraised against four newly challenging algorithms and the other recently reported optimizers in the literature under fair comparisons, to prove its superiority. Particularly, the minimum values of the SSDs for Ballard Mark, BCS 0.5 kW, NedStack PS6, and Temasek 1 kW PEMFCs stacks are 0.810578 V2, 0.0116952 V2, 2.10847 V2, and 0.590467 V2, respectively. Furthermore, the performance measures are evaluated on various metrics. Lastly, a simplified trial to upgrade Amphlett’s model to include the PEMFCs’ electrical dynamic response is introduced. The KOA appears to be viable and may be extended in real-time conditions according to the presented scenarios (steady-state and transient conditions).
Ultrastructure of noise-induced cochlear synaptopathy
Authors: Moverman Daniel J. , Liberman Leslie D. , Kraemer Stephan , Corfas Gabriel , Liberman M. Charles 
Published: November 2023

AbstractAcoustic overexposure can eliminate synapses between inner hair cells (IHCs) and auditory nerve fibers (ANFs), even if hair-cell function recovers. This synaptopathy has been extensively studied by confocal microscopy, however, understanding the nature and sequence of damage requires ultrastructural analysis. Here, we used focused ion-beam scanning electron microscopy to mill, image, segment and reconstruct ANF terminals in mice, 1 day and 1 week after synaptopathic exposure (8–16 kHz, 98 dB SPL). At both survivals, ANF terminals were normal in number, but 62% and 53%, respectively, lacked normal synaptic specializations. Most non-synapsing fibers (57% and 48% at 1 day and 1 week) remained in contact with an IHC and contained healthy-looking organelles. ANFs showed a transient increase in mitochondrial content (51%) and efferent innervation (34%) at 1 day. Fibers maintaining synaptic connections showed hypertrophy of pre-synaptic ribbons at both 1 day and 1 week. Non-synaptic fibers were lower in mitochondrial content and typically on the modiolar side of the IHC, where ANFs with high-thresholds and low spontaneous rates are normally found. Even 1 week post-exposure, many ANF terminals remained in IHC contact despite loss of synaptic specializations, thus, regeneration efforts at early post-exposure times should concentrate on synaptogenesis rather than neurite extension.
Mitigation of biogenic methanethiol using bacteriophages in synthetic wastewater augmented with Pseudomonas putida
Authors: Sarat Niti , Salim Amrita , Pal Sanjay , Subhash Suja , Prasad Megha , Nair Bipin G. , Madhavan Ajith 
Published: November 2023

AbstractWastewater malodour is the proverbial ‘elephant in the room’ notwithstanding its severe implications on sanitation, health, and hygiene. The predominant malodorous compounds associated with wastewater treatment plants and toilets are volatile organic compounds, such as hydrogen sulphide, ammonia, methanethiol, and organic acids. Among them, methanethiol warrants more attention owing to its relatively low olfactory threshold and associated cytotoxicity. This requires an efficient odour-abatement method since conventional techniques are either cost-prohibitive or leave recalcitrant byproducts. Bacteriophage-based methodology holds promise, and the described work explores the potential. In this study, a non-lysogenous Pseudomonas putida strain is used as a model organism that produces methanethiol in the presence of methionine. Two double-stranded DNA phages of genome sizes > 10 Kb were isolated from sewage. ɸPh_PP01 and ɸPh_PP02 were stable at suboptimal pH, temperature, and at 10% chloroform. Moreover, they showed adsorption efficiencies of 53% and 89% in 12 min and burst sizes of 507 ± 187 and 105 ± 7 virions per cell, respectively. In augmented synthetic wastewater, ɸPh_PP01 and ɸPh_PP02 reduced methanethiol production by 52% and 47%, respectively, with the concomitant reduction in P. putida by 3 logs in 6 h. On extension of the study in P. putida spiked-sewage sample, maximum reduction in methanethiol production was achieved in 3 h, with 49% and 48% for ɸPh_PP01 and ɸPh_PP02, respectively. But at 6 h, efficiency reduced to 36% with both the phages. The study clearly demonstrates the potential of phages as biocontrol agents in the reduction of malodour in wastewater.