syedzayyan/paper_mill_benchmark huggingface dataset:
Zero-Shot Human-Object Interaction Detection via Similarity Propagation.

Human-object interaction (hoi) detection involves identifying interactions represented as [formula: see text] , requiring the localization of human-object pairs and interaction classification within an image.This work focuses on the challenge of detecting hois with unseen objects using the prevalent transformer architecture.Our empirical analysis reveals that the performance degradation of novel hoi instances primarily arises from misclassifying unseen objects as confusable seen objects.To address this issue, we propose a similarity propagation (sp) scheme that leverages cosine similarity distance to regulate the prediction margin between seen and unseen objects.In addition, we introduce pseudo-supervision for unseen objects based on class semantic similarities during training.Furthermore, we incorporate semantic-aware instance-level and interaction-level contrastive losses with transformer to enhance intraclass compactness and interclass separability, resulting in improved visual representations.Extensive experiments on two challenging benchmarks, v-coco and hico-det, demonstrate the effectiveness of our model, outperforming current state-of-the-art methods under various zero-shot settings.

Journal: IEEE transactions on neural networks and learning systems (2023)
Publication types: Journal Article
Development and Validation of an Instrument for Measuring Parenting Stress among Clinical Nurses.

Clinical nurses who are mothers of preschool-aged children experience extreme parenting stress linked to their hospital work environment and shift work, differing from that generally experienced by mothers.This study aimed to develop and validate a parenting stress scale that considers the clinical nurses' form of work and its characteristics.Methods the scale items were initially derived from in-depth interviews and a literature review and were revised and modified based on the results of content validity testing by experts.The developed instrument was evaluated using data from 157 clinical nurses in south korea who were mothers of preschool-aged children.Results in the instrument validation stage, 19 items categorized in four factors (psychological burden, physical and mental fatigue, work shift, and work environment) were derived from construct validity, and the cumulative explanatory power was 56.6%.Furthermore, the convergent and discriminant validity and external construct were confirmed.Cronbach's α of the final instrument was .86 (range: .81-.86).The validity and reliability of the newly developed parenting stress scale for clinical nurses were established in this study; it uses a 4-point likert scale.A higher mean score by factor indicates a higher level of parenting stress experienced by clinical nurses.Conclusion this instrument would be beneficial to measure the level of parenting stress among nurses who work in hospitals and evaluate factors related to their parenting stress to devise effective interventions.

Journal: Asian nursing research (2021)
Publication types: Journal Article
Threads in tubing: an innovative approach towards improved electrochemical thread-based microfluidic devices.

Thread-based microfluidic analytical devices have received growing attention since threads have some advantages over other materials.Compared to paper, threads are also capable of spontaneously transporting fluid due to capillary action, but they have superior mechanical strength and do not require hydrophobic barriers.Therefore, thread-based microfluidic devices can be inexpensively fabricated with no need for external pumps or sophisticated microfabrication apparatus.Despite these outstanding features, achieving a controlled and continuous flow rate is still a challenging task, mainly due to fluid evaporation.Here, we overcome this challenge by inserting a cotton thread into a polyethylene tube aiming to minimize fluid evaporation.Also, a cotton piece was inserted into the outlet reservoir to improve the wicking ability of the device.This strategy enabled the fabrication of an innovative electrochemical thread in a tubing microfluidic device that was capable to hold a consistent flow rate (0.38 μl s-1) for prolonged periods, allowing up to 100 injections in a single device by simply replacing the cotton piece in the outlet reservoir.The proposed device displayed satisfactory analytical performance for selected model analytes (dopamine, hydrogen peroxide, andtert-butylhydroquinone), in addition to being successfully used for quantification of nitrite in spiked artificial saliva samples.Beyond the flow rate improvement, this "thread-in-tube" strategy ensured the protection of the fluid from external contamination while making it easier to connect the electrode array to the microchannels.Thus, we envision that the thread in a tube strategy could bring interesting improvements to thread-based microfluidic analytical devices.

Journal: Lab on a chip (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A multi-modal algorithm based on an NSGA-II scheme for phylogenetic tree inference.

The analysis of evolutionary data allows uncovering information about the organisms and how they have adapted and evolved.This information could provide us with new insights about the specialisation of organisms (or part of them), how they adapt, how similar they are with other species, among others.Unfortunately, this evolutionary history can only be estimated, and for that, several computational methods exist.Among the methods, optimisation methods are one of the main approaches to deal with this problem, with multiobjective optimisation producing promising results.In this paper, we deal with multiobjective phylogenetic inference, using a multi-modal metaheuristic approach that exploits the decision space in the multiobjective formulation of the problem.In particular, we incorporate a new metric based on a topological tree distance.We compare the method with state of the art algorithms in terms of performance.Additionally, we perform a thorough analysis of a study case on a yeast saccharomyces cerevisiae dataset.Results show that our proposal is able to improve the diversity of solutions while improving or keeping the quality of solutions in terms of hypervolume.

Journal: Bio Systems (2022)
Publication types: Journal Article
Geographic and position-based variations in phyllospheric bacterial communities present on flue-cured tobacco.

Although tobacco leaves (tls) contain abundant bacteria, how the geography and leaf position of tls affect these bacteria is unclear.Here, tls at different positions from henan (hn, strong flavor style) and yunnan (yn, fresh flavor style) provinces were collected, and the bacteria were characterized by illumina sequencing at harvest and 1 year of storage.Bacterial communities were very different between tls originating from different geographical areas and positions, and beta diversity analysis showed that leaf position was the most important factor for phyllospheric bacterial communities, followed by geographical area and storage time.At the genus level, subdoligranulum, thermus, and acinetobacter were obviously more abundant in hn than in yn, while blautia and ruminococcus were significantly more abundant in yn.These differences in bacterial communities decreased after 1 year of storage, indicating that the microbiota tends to become similar during tobacco processing.Storage time also affected the phyllospheric bacteria of tls, as the bacterial communities shifted significantly on both hn and yn tls after 1 year of storage.Significant differences in the predicted genes were also observed between the different geographic locations and leaf positions.Potential human pathogens, including acinetobacter, methylobacterium, and escherichia-shigella, were greatly different between tls originating from different areas and positions.These data suggested that geographic variations and positions were associated with phyllospheric bacterial communities on tls, which may be related to not only the flavor style and quality of tls but also the potential health risks to humans.Key points: • tobacco leaf position and tobacco growth location affected bacterial communities.• microbial communities of tls shifted significantly after one year of storage.• potential human pathogens differed at different leaf positions and growth locations.

Journal: Applied microbiology and biotechnology (2021)
Publication types: Journal Article
Fixational stability as a measure for the recovery of visual function in amblyopia.

People with amblyopia have been shown to have decreased fixational stability, particularly those with strabismic amblyopia.Fixational stability and visual acuity have been shown to be tightly correlated across multiple studies, suggesting a relationship between acuity and oculomotor stability.Reduced visual acuity is the sine qua non of amblyopia, and recovery is measured by the improvement in visual acuity.Here we ask whether fixational stability can be used as an objective marker for the recovery of visual function in amblyopia.We tracked children's fixational stability during patching treatment over time and found fixational stability changes alongside improvements in visual acuity.This suggests fixational stability can be used as an objective measure for monitoring treatment in amblyopia and other disorders.

Journal: Proceedings. Eye Tracking Research & Applications Symposium (2021)
Publication types: Journal Article
Automated Shoulder Implant Manufacturer Detection using Encoder Decoder based Classifier from X-ray Images.

Total shoulder arthroplasty is the process of replacing the damaged ball and socket joint in the shoulder with a prosthesis made with polyethylene and metal components.The prosthesis helps to restore the normal range of motion and reduce pain, enabling the patient to return to their daily activities.These implants may need to be replaced over the years due to damage or wear and tear.It is a tedious and time-consuming process to identify the type of implant if medical records are not properly maintained.Artificial intelligence systems can speed up the treatment process by classifying the manufacturer and model of the prosthesis.We have proposed an encoder-decoder based classifier along with the supervised contrastive loss function that can identify the implant manufacturer effectively with increased accuracy of 92% from x-ray images overcoming the class imbalance problem.

Journal: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference (2023)
Publication types: Journal Article
In situ investigation of acute exposure of graphene oxide on activated sludge: Biofilm characteristics, microbial activity and cytotoxicity.

Graphene oxide (go) has wide applications in many fields which has caused a large expected quantity of the graphene-based wastes.It is necessary to understand the toxic effects of the go on the activated sludge (as) considering its inevitable discharge to the wastewater treatment plants as the ultimate repositories for these wastes.In this study, the acute exposures of the multilayer nano-graphene oxide (mngo) at different dosages were conducted in order to investigate its integrated effects on the formation of the biofilm, mature biofilm and the microbial activity of the activated sludge.Raman spectroscopy and laser scanning confocal microscopy (lscm) were adopted for the in-situ characterization of the biofilm with the exposure of the mngo.The results showed that the activated sludge was tolerable to the acute exposure of the less than 100 mg/l of the mngo, especially for the mature biofilm, and only a subtle decrease was found in the size and thickness during the formation of the biofilm, while the amount of 300 mg/l of the mngo caused the sever deterioration on the activated sludge system.The microbial metabolic activity, viability, and the biological removal of the nutrients were significantly affected with the more than 100 mg/l of the mngo.It was also demonstrated by the microbial cytotoxicity tests that the increase in the exposure of the mngo was related to the increase in the reactive oxygen species (ros) and the damaging degree of the cell membrane.

Journal: Ecotoxicology and environmental safety (2020)
Publication types: Journal Article
Clinical Profile and Treatment Outcome in MOGAD: A Single-Center Case-Series Study in Guiyang, China.

The clinical spectrum of myelin oligodendrocyte glycoprotein antibody-associated disease (mogad) is expanding over time.However, the long-term management and prognosis of this disorder are still controversial.Therefore, this study aimed to report the clinical profiles and treatment outcomes of mogad in our center.Methods this was a single-center case-series study.Clinical and para-clinical data, along with treatment outcomes of patients with mogad were analyzed.Results a total of 27 patients were identified, of which 19 (70%) patients were women, and the median age at disease onset was 40 years (range 20-67).A total of 47 episodes were observed, with optic neuritis (53%) being the most frequent presentation and 60% of them were unilateral.Other presentations included rhombencephalitis (re) (17%), limbic encephalitis (9%), simultaneous optic neuritis and myelitis (9%), acute disseminated encephalomyelitis (adem)-like presentation (6%), myelitis (4%), and adem (2%).One patient presenting with re also met the diagnostic criteria of area postrema syndrome (aps).Another patient with re presented with imaging characteristics of chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (clippers).A total of 29 lumbar punctures were recorded, among which an elevated protein level was found in 34% of the samples, pleocytosis was found in 14% of the samples, and positive intrathecal oligoclonal bands were found in 19% of the patients.One patient was found to have anti-n-methyl-d-aspartate receptor antibodies both in his serum and cerebrospinal fluid.Intravenous methylprednisolone (ivmp) was administrated for 85% of the attacks while both ivmp and intravenous immunoglobulin were for 6% of the attacks.Moreover, nine patients received maintenance therapy.Among them, six patients were treated with mycophenolate mofetil, three patients were treated with prednisone, rituximab, and teriflunomide, respectively.The median follow-up period was 20 months (range 6-127).At follow-up, twelve (44%) patients experienced a relapsing course, and the median time to the first relapse was 9.5 months (range 2-120).The median expanded disability status scale score at nadir was 3.5 (range 2-8) and was 0 (range 0-3) at the last follow-up.Conclusion the clinical spectrum of mogad is heterogenous, wherein aps and clippers-form can occur.The long-term outcome of mogad seems benign.Further studies are warranted to determine the risk factors of relapse and identify the optimal steroid-sparing agents.

Journal: Frontiers in neurology (2022)
Publication types: Journal Article
Changes in alcohol use and heavy episodic drinking in U.S. Women of childbearing-age and peripartum between 2001-2002 and 2012-2013.

Heavy episodic drinking (hed) is a frequent pattern of alcohol use in women of childbearing age with severe consequences for both women and child, making it a major public health issue.Some states in the us have reported laws that target the use of alcohol during pregnancy.Our aim was to examine the evolution of 12-month alcohol use and 12-month hed prevalence in childbearing age, pregnant and postpartum women between 2001 and 2002 and 2012-2013.Methods our data were drawn from the national epidemiologic study of alcohol and related conditions (nesarc) conducted in 2001-2002 and nesarc-iii conducted in 2012-2013, two independent, representative samples of u.s.Population past-year alcohol use and hed was evaluated according face-to-face interview for all participants.Results our sample consisted of 24,536 women of childbearing age, including 2846 pregnant and postpartum women.Prevalence of 12-month alcohol use increased from 2001 to 2002 to 2012-2013, in both childbearing-aged women (66.14% to 75.48%; a or = 1.62, 95%ci = 1.46-1.80) and pregnant and postpartum women (57.81% to 66.19%; a or = 1.56, 95%ci = 1.25-1.94).Prevalence of 12-month hed increased from 2001 to 2002 to 2012-2013, in both childbearing-aged women (22.57% to 36.34%; a or = 1.97, 95%ci = 1.79-2.16) and pregnant and postpartum women (17.85% to 28.21%; a or = 1.84, 95%ci = 1.47-2.30).Conclusions alcohol use and hed increased in last 10 years in both childbearing age and pregnant and postpartum us women.That questions the impact of implemented laws, policies and alcohol guidelines in this population within the last 10 years.

Journal: Addictive behaviors (2020)
Publication types: Journal Article
Molecular testing in non-small cell lung cancer: A consensus recommendation.

Introduction lung cancer remains an important cause of cancer-related mortality in singapore, with a greater proportion of non-smokers diagnosed with non-small cell lung cancer (nsclc) in the past 2 decades.The higher prevalence of targetable genomic alterations in lung cancer diagnosed in singapore compared with countries in the west, as well as the expanding therapeutic landscape for nsclc in the era of precision medicine, are both factors that underscore the importance of efficient and effective molecular profiling.Method this article provides consensus recommendations for biomarker testing for early-stage to advanced nsclc.These recommendations are made from a multidisciplinary group of lung cancer experts in singapore with the aim of improving patient care and long-term outcomes.Results the recommendations address the considerations in both the advanced and early-stage settings, and take into account challenges in the implementation of biomarker testing as well as the limitations of available data.Biomarker testing for both tumour tissue and liquid biopsy are discussed.Conclusion this consensus statement discusses the approaches and challenges of integrating molecular testing into clinical practice for patients with early- to late-stage nsclc, and provides practical recommendations for biomarker testing for nsclc patients in singapore.

Journal: Annals of the Academy of Medicine, Singapore (2023)
Publication types: Journal Article;Review
Active Antioxidant Phenolics from Brazilian Red Propolis: An Optimization Study for Their Recovery and Identification by LC-ESI-QTOF-MS/MS.

Brazilian red propolis (brp) is a natural product widely known for its phenolic composition and strong antioxidant properties.In this study, we used the box-behnken design (bbd) with surface response methodology to optimize the extraction conditions for total phenolic content (tpc) and trolox equivalent antioxidant capacity(teac) of bioactive phenolics from brp.The extraction time, ethanol/water concentration and temperature, were tested.All variables had significant effects (p≤ 0.05), with a desirability coefficient of 0.88.Under optimized conditions (90% ethanol at 80 °c for 30 min), the brp extract showed a tpc of 129.00 ± 2.16 mg gae/g and a teac of 3471.76 ± 53.86 μmol te/g.Moreover, frap and orac assays revealed that the optimized brp extract had 1472.86 ± 72.37 μmol fe2+/g and 4339.61 ± 114.65 μmol te/gof dry weight, respectively.Thirty-two phenolic compounds were tentatively identified by lc-qtof-esi-ms/ms, of which thirteen were found for the first time in brp, including four flavones, one flavanol, two flavanones, two chalcones, and four isoflavonoids.Thus, our results highlight the importance of brp as a source of a wide variety of phenolic compounds with significant antioxidant properties.

Journal: Antioxidants (Basel, Switzerland) (2021)
Publication types: Journal Article
Potential role of carvedilol in intestinal toxicity through NF-κB/iNOS/COX-2/TNF-α inflammatory signaling pathway in rats.

The increased use of indomethacin (ind) is associated with gastrointestinal injury.This research aims to investigate the effects of a beta-blocker, carvedilol (car) on a rat model of ind-induced acute intestinal damage and clarify the probable underlying protective mechanisms.Materials and methods twenty-four male wistar rats were divided into four groups.Control group: given vehicles; car-treated group: given 10 mg/kg/day car po daily by gastric gavage for 10 consecutive days; ind-treated group: given a single sc dose of 10 mg/kg ind at the end of the ninth day of the experiment; combined car/ind-treated group: given both ind and car.Results in the rats that received ind, severe intestinal histopathological changes together with oxidative and nitrosative intestinal stress were present biochemically and immunohistochemically.Obvious inflammatory and tissue damage were represented by the significant intestinal increases in tnf-α, cox-2, and caspase-3 together with the elevated expression of vcam-1 adhesion molecules.Intestinal gene expression of nf-k b and cox-2 was also increased.Pretreatment with car significantly reversed the ind-induced intestinal toxic manifestations.Conclusion car has beneficial intestinal protective effects.Its ameliorative action is conferred through its antioxidant, antinitrosative, anti-inflammatory, and antiapoptotic properties.

Journal: Immunopharmacology and immunotoxicology (2022)
Publication types: Journal Article
Inhibition of triple negative breast cancer metastasis and invasiveness by novel drugs that target epithelial to mesenchymal transition.

Invasive breast cancer (br ca) is predicted to affect 1 in 9 women in a lifetime;1 in 32 will die from this disease.The most aggressive forms of br ca, basal-like/triple-negative phenotype (tnbc), are challenging to treat and result in higher mortality due high number of metastatic cases.There is a paucity of options for tnbc treatment, which highlights the need for additional innovative treatment approaches.Nih-iii mice were injected in the abdominal mammary fat pad with luciferase-expressing derivative of the human tnbc cell line, mda-mb-231 cells.Animals were gavage-fed with nitrofen at the doses of 1, 3 or 6 mg/kg/alternate days.However, several structural properties/components of nitrofen raise concerns, including its high lipophilicity (c log p of nearly 5) and a potential toxophore in the form of a nitroarene group.Therefore, we developed analogues of nitrofen which lack the nitro group and/or have replaced the diaryl ether linker with a diarylamine that could allow modulation of polarity.In vitro anti-invasiveness activity of nitrofen analogues were evaluated by quantitative determination of invasion of mda-mb-231-luciferase cells through matrigel using a boyden chamber.Our in vivo data show that nitrofen efficiently blocks tnbc tumor metastasis.In vitro data suggest that this is not due to cytotoxicity, but rather is due to impairment of invasive capacity of the cells.Further, using an in vitro model of emt, we show that nitrofen interferes with the process of emt and promotes mesenchymal to epithelial transformation.In addition, we show that three of the nitrofen analogues significantly reduced invasive potential of tnbc cells, which may, at least partially, be attributed to the analogues' ability to promote mesenchymal to epithelial-like transformation of tnbc cells.Our study shows that nitrofen, and more importantly its analogues, are significantly effective in limiting the invasive potential of tnbc cell lines with minimal cytotoxic effect.Further, we demonstrate that nitrofen its analogues, are very effective in reversing mesenchymal phenotype to a more epithelial-like phenotype.This may be significant for the treatment of patients with mesenchymal-tnbc tumor subtype who are well known to exhibit high resistance to chemotherapy.

Journal: Scientific reports (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't