PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations.

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.

Caffeine Consumption and Depression, Anxiety, and Stress Levels Among University Students in Medina: A Cross-Sectional Study.

Introduction Caffeine is a psychoactive stimulant frequently found in coffee, tea, energy drinks, and some medications. Various mental health challenges, including stress, anxiety, and depression, commonly affect college students. Moreover, an individual's mental and physical health can be significantly impacted by stress, anxiety, and depression. However, the impact of caffeine on mental health, particularly its association with depressive and anxiety symptoms, remains inconclusive. Thus, this study aimed to evaluate the amount of caffeine consumed by university students and its association with depression, anxiety, and stress levels. Material and method This cross-sectional study was performed on Taibah University students in Medina from both health-related and non-health-related colleges. We used a self-administrated questionnaire composed of four sections: the informed consent section; sociodemographic information; the Depression, Anxiety, and Stress Scale (DASS-21), which assessed the depression, anxiety, and stress levels; and a caffeine-measuring questionnaire, which reported daily caffeine intake in milligrams per day. Result This cross-sectional study examined a 520 convenience sample of Taibah University students with an age range from 17 to 29 years. The majority of the participants were single (95.2%), most of them were female (73.8%), and slightly more than half (51.5%) were recruited from health-related colleges. According to the study's DASS-21 score results, 45.8% of the students had extremely severe stress, 61% had extremely severe anxiety, and 51% had extremely severe depression. The most frequently reported sources of daily caffeine among the participants were Arabic coffee (69.6%), specialty coffee (57.5%), black tea (56.3%), cola (48.7%), and regular coffee (48.5%). The overall daily amount of consumed caffeine ranged from zero to 4276.7 mg/oz. However, no significant association was found between the severity of the DASS-21 score and the daily consumption of caffeine among Taibah University students. Conclusion Our study shows no significant association between the severity of depression, anxiety, and stress and daily caffeine consumption among university students. This proves the opposite of the theory that high levels of caffeine consumption can be correlated to high levels of depression, stress, and anxiety.

A Rare Case of Rhupus Syndrome With Systemic Involvement: A Case Report and Literature Review.

Based on clinical signs, symptoms, radiological, and serological findings, a 37-year-old woman was diagnosed with an overlap between rheumatoid arthritis and systemic lupus erythematosus, referred to as rhupus syndrome. Her condition was complicated by lupus nephritis, autoimmune hemolytic anemia, and central nervous system (CNS) vasculitis. She improved after receiving steroids, hydroxyquinone, and cyclophosphamide. There are no established criteria for diagnosing rhupus syndrome. Being aware of autoimmunity and overlapping illness signs and using specific diagnostic tests are crucial. Early therapy may avoid irreversible organ damage.

Comparison of bone mineral density and Fracture Risk Assessment Tool in Saudi women with and without type 2 diabetes mellitus: A cross-sectional study.

OBJECTIVES: To compare the bone mineral density and the fracture risks in Saudi women with and without type 2 diabetes mellitus (T2DM). METHODS: This cross-sectional study was carried out at Taibah Early Diagnostic Center, Al Madinah Al Munawarah, Saudi Arabia. A total of 465 women with and without T2DM aged ≥40 years who visited the center for a dual-energy X-ray absorptiometry scan between December 2020 and July 2021 were randomly selected. The 10-year probabilities of major osteoporotic fracture (MOF) and hip fracture (HF) were calculated using the Abu Dhabi Fracture Risk Assessment Tool (FRAX) with and without adjustment for T2DM. The adjustment was made by setting rheumatoid arthritis as the equivalent risk for T2DM in the FRAX. Bone mineral density values and the FRAX scores were compared between women with T2DM and non-diabetes. RESULTS: Of 465 women, 214 had T2DM, and 251 were non-diabetics. The mean age of women was 59.42±7.9 years. There were no significant differences in mean age, menopausal status, height, weight, and body mass index between T2DM and non-diabetic women. Bone mineral density values and the unadjusted FRAX scores were comparable between the 2 groups. However, after adjusting FRAX for T2DM, the FRAX for MOF and HF became significantly higher in T2DM women (p=0.000 and p=0.004). CONCLUSION: In Saudi women with T2DM, unadjusted FRAX underestimated the risk of MOF and HF. Type 2 diabetes mellitus should be included as one of the clinical risk factors for fracture in future versions of the FRAX score.

Self-Nanoemulsifying Drug Delivery System (SNEDDS) of Apremilast: In Vitro Evaluation and Pharmacokinetics Studies.

Psoriatic arthritis is an autoimmune disease of the joints that can lead to persistent inflammation, irreversible joint damage and disability. The current treatments are of limited efficacy and inconvenient. Apremilast (APR) immediate release tablets Otezla® have 20-33% bioavailability compared to the APR absolute bioavailability of 73%. As a result, self-nanoemulsifying drug delivery systems (SNEDDS) of APR were formulated to enhance APR's solubility, dissolution, and oral bioavailability. The drug assay was carried out using a developed and validated HPLC method. Various thermodynamic tests were carried out on APR-SNEDDS. Stable SNEDDS were characterized then subjected to in vitro drug release studies via dialysis membrane. The optimum formulation was F9, which showed the maximum in vitro drug release (94.9%) over 24 h, and this was further investigated in in vivo studies. F9 was composed of 15% oil, 60% Smix, and 25% water and had the lowest droplet size (17.505 ± 0.247 nm), low PDI (0.147 ± 0.014), low ZP (-13.35 mV), highest %T (99.15 ± 0.131) and optimum increases in the relative bioavailability (703.66%) compared to APR suspension (100%) over 24 h. These findings showed that APR-SNEDDS is a possible alternative delivery system for APR. Further studies are warranted to evaluate the major factors that influence the encapsulation efficiency and stability of APR-containing SNEDDS.

Artificial Intelligence and Machine Learning in Optical Information Processing: introduction to the feature issue.

This special feature issue covers the intersection of topical areas in artificial intelligence (AI)/machine learning (ML) and optics. The papers broadly span the current state-of-the-art advances in areas including image recognition, signal and image processing, machine inspection/vision and automotive as well as areas of traditional optical sensing, interferometry and imaging.

Root and Canal Morphology of Mandibular Premolars in a Saudi Subpopulation: A Cone-Beam Computed Tomography Study.

Objectives: The efficacy of root canal therapy is dependent on a thorough understanding of both normal and aberrant root canal morphology. As a result, the purpose of this study was to use CBCT to characterize the exact root and canal morphology of mandibular premolars in a Saudi subpopulation. Methods: The current study included 1000 mandibular premolars (507 first premolars and 493 second premolars) with completely developed roots. CBCT was performed to assess the shape of the roots and to classify the canal anatomy according to Vertucci's classification. The incidence and similarity of the left and right sides, as well as men and women, were investigated. The data were examined using the chi-square test. Results: Of the 507 mandibular first premolars analyzed, 484 (95.5%) had one root, whereas 23 (4.5%) had two roots. Of the 493 mandibular second premolars analyzed, 489 (99.2%) had one root, whereas four teeth had two roots (0.8%). There were no statistically significant variations in the number of roots identified across groups (p > 0.05). The most prevalent in mandibular first premolars was type I, accounting for 70.0% (n = 355) of the studied sample, followed by type II (14.2%, n = 72) and type IV (10.1%, n = 51). For mandibular second premolar, type I had the highest incidence (449 (91.1%)), followed by type II (5.7%, n = 28). Conclusion: In a Saudi subpopulation, the majority of mandibular first and second premolar teeth had a single root with a type I canal system. On the other hand, numerous roots with various canal classifications were found.

Assessment of root morphology and canal configuration of maxillary premolars in a Saudi subpopulation: a cone-beam computed tomographic study.

BACKGROUND: The objective of this study was to use CBCT to look into the root canal morphology of maxillary premolars in a Saudi Arabian subpopulation and associate the results to existing canal morphology classifications. METHODS: The sample size for this analysis was 500 right and left untreated maxillary first and second premolars with fully formed roots from 250 Saudi residents (125 male and 125 female). The following observations were made using CBCT on the teeth related: (1) The number and morphology of roots; (2) The canal morphology for each root according to Vertucci's classification. The frequency and similarities between the right and left sides, as well as between females and males, were studied. The Chi-square test was used to assess the results. RESULTS: Of the 500 maxillary first premolars studied, 199 teeth had one root (39.8%), whilst 293 (58.6%) were two-rooted. Three-rooted maxillary first premolars were found in 8 (1.6%). For maxillary second premolars, 416 premolars had one root (83.2%), whilst 79 (15.8%) had two roots and the rest 5 (1.0%) were three roots. There were significant differences of number of root were found between groups (p > 0.05). For maxillary first premolar, Type IV was the most frequent, accounting for 57.8% of the sample (n = 289), followed by type II (32.8%, n = 164). For maxillary second premolar, Type I was mainly occurrence 302 (60.4%), followed by Type II (16.4%, n = 82). CONCLUSIONS: The majority of maxillary first premolars had two roots and two root canals, while one root and one root canal was the most common anatomical configuration for maxillary second premolars. Additional canal forms do occur on occasion, and clinicians should pay close attention to them.

Patients' Knowledge and Perceived Barriers toward Replacement of Missing Teeth among Respondents of Hail City, Kingdom of Saudi Arabia.

AIM: Teeth maintain the functionality and esthetic of oral cavity, they are also important for psychological and social well-being. This study aims to assess awareness of patients toward replacement of missing teeth. People with unrestored or missing teeth tend to have poor self-esteem and oral health-related quality of life; hence, their knowledge toward restoring and replacing teeth is an important aspect to be measured. MATERIALS AND METHODS: It was an observational study having a cross-sectional design. Face- and content-validated questionnaire was used as study tool. Nonprobability, convenient sampling technique was employed that yielded information from 183 respondents residing in various areas of Hail city. Data were collected after written informed consent. The study was approved by the University of Hail ethical committee. RESULTS: Two hundred questionnaires were distributed, out of which 183 were returned. Regarding knowledge of restoring missing teeth, 145 (79.2%) respondents know that function and esthetic can be maintained by replacing missing teeth. Information about the availability of various types of prosthesis was mostly obtained by them through their dentist (70; 48.3%), while books/magazines/Internet was the second source (38; 26.2%) and 37 (25.5%) heard it from someone who has already undergone the replacement of teeth. CONCLUSION: The present study indicated that a good number of respondents have the knowledge of teeth replacement, and dentists were the most common source of information to the patients in terms of education about different treatment options. CLINICAL SIGNIFICANCE: Evaluate and plan treatment options based on patients' expectations and perceptions.

Saliva as a diagnostic tool for oral and systemic diseases.

Early disease detection is not only vital to reduce disease severity and prevent complications, but also critical to increase success rate of therapy. Saliva has been studied extensively as a potential diagnostic tool over the last decade due to its ease and non-invasive accessibility along with its abundance of biomarkers, such as genetic material and proteins. This review will update the clinician on recent advances in salivary biomarkers to diagnose autoimmune diseases (Sjogren's syndrome, cystic fibrosis), cardiovascular diseases, diabetes, HIV, oral cancer, caries and periodontal diseases. Considering their accuracy, efficacy, ease of use and cost effectiveness, salivary diagnostic tests will be available in dental offices. It is expected that the advent of sensitive and specific salivary diagnostic tools and the establishment of defined guidelines and results following rigorous testing will allow salivary diagnostics to be used as chair-side tests for several oral and systemic diseases in the near future.

Nociception and role of immune system in pain.

Both pain and inflammation are protective responses. However, these self-limiting conditions (with well-established negative feedback loops) become pathological if left uncontrolled. Both pain and inflammation can interact with each other in a multi-dimensional manner. These interactions are known to create an array of 'difficult to manage' pathologies. This review explains in detail the role of immune system and the related cells in peripheral sensitization and neurogenic inflammation. Various neuro-immune interactions are analyzed at peripheral, sensory and central nervous system levels. Innate immunity plays a critical role in central sensitization and in establishing acute pain as chronic condition. Moreover, inflammatory mediators also exhibit psychological effects, thus contributing towards the emotional elements associated with pain. However, there is also a considerable anti-inflammatory and analgesic role of immune system. This review also attempts to enlist various novel pharmacological approaches that exhibit their actions through modification of neuro-immune interface.

Matrix metalloproteinases and their pathological upregulation in multiple sclerosis: an overview.

Matrix metalloproteinases (MMPs) are a family of extracellular proteases associated with extracellular matrix remodeling. They are involved in many physiological and reparative processes. MMPs can break down all extracellular constituents; therefore, their expression is very tightly regulated and their abnormal activity or over production has been linked to many diseases including multiple sclerosis (MS) which is a leading cause of non-traumatic disability in young adults in North America. Recently many studies, both in animals and humans, have been conducted to better elucidate the underlying causes, mechanisms and pathophysiology of MS. In this review, we discuss the potential role of pathological upregulation of MMPs in MS and future challenges which if properly addressed might help in development of potential cure for this disease.

Laparoscopic removal of a copper intrauterine device from the sigmoid colon.

IUD translocation to the sigmoid colon after uterine perforation is a rare but serious event. Removal of the IUD in such a situation has been recommended because of the risk of complication, such as fistula formation and colonic perforation. We present the case of a 43-year-old female with a copper T380A IUD embedded in the sigmoid colon, which was removed with minimally invasive techniques.

What can we learn from the shape of a correlation peak for position estimation?

Matched filtering is a robust technique to identify and locate objects in the presence of noise. Traditionally, the amplitude of the correlation peak is used for detection of a match. However, when distinguishing objects that are not significantly different or detecting objects under high noise imaging conditions, the normalized peak amplitude alone may not provide sufficient discrimination. In this paper, we demonstrate that measurements derived from the shape of the correlation peak offer not only higher levels of discrimination but also accurate position estimation. To our knowledge, this is the first time such features have been used in a real-time system, like the National Ignition Facility, where such techniques enable real-time, accurate position estimation and alignment under challenging imaging conditions. It is envisioned that systems utilizing matched filtering will greatly benefit from incorporating additional shape based information.

Artificial neural networks using complex numbers and phase encoded weights.

The model of a simple perceptron using phase-encoded inputs and complex-valued weights is proposed. The aggregation function, activation function, and learning rule for the proposed neuron are derived and applied to Boolean logic functions and simple computer vision tasks. The complex-valued neuron (CVN) is shown to be superior to traditional perceptrons. An improvement of 135% over the theoretical maximum of 104 linearly separable problems (of three variables) solvable by conventional perceptrons is achieved without additional logic, neuron stages, or higher order terms such as those required in polynomial logic gates. The application of CVN in distortion invariant character recognition and image segmentation is demonstrated. Implementation details are discussed, and the CVN is shown to be very attractive for optical implementation since optical computations are naturally complex. The cost of the CVN is less in all cases than the traditional neuron when implemented optically. Therefore, all the benefits of the CVN can be obtained without additional cost. However, on those implementations dependent on standard serial computers, CVN will be more cost effective only in those applications where its increased power can offset the requirement for additional neurons.

A structured review and theme analysis of papers published on 'quality of life' in head and neck cancer: 2000-2005.

Over the past 10 years, quality of life (QOL) has been increasingly recognised as an important outcome parameter in head and neck cancer. Validated questionnaires have emerged and there has been an increase in the number of papers published each year. The aim of this article is to review the literature over the past five years (2000-2005 inclusive), to identify papers reporting outcomes using patient self-competed questionnaires and group these into themes. The tabulated summary allows for the areas of health related quality of life research to be identified and to explore issues that are perhaps deficit in the literature. The three authors independently searched the literature published in the English language using the ISI search engine with cross-reference using Pub Med and Ovid. The search terms were; quality of life, questionnaire, and head and neck cancer. Studies were placed in to one of five themes. There were 165 studies identified. The numbers in each theme were predictors of QOL [Hassanein KA, Musgrove BT, Bradbury E. Functional status of patients with oral cancer and its relation to style of coping, social support and psychological status. Br J Oral Maxillofac Surg 2001;39:340-5.], functional outcome [Klug C, Neuburg J, Glaser C, Schwarz B, Kermer C, Millesi W. Quality of life 2-10 years after combined treatment for advanced oral and oropharyngeal cancer. Int J Oral Maxillofac Surg 2002;31:664-9.], questionnaire development [Hanna E, Sherman A, Cash D, Adams D, Vural E, Fan CY, et al. Quality of life for patients following total laryngectomy vs chemoradiation for laryngeal preservation. Arch Otolaryngol Head Neck Surg 2004;130:875-9.], randomised clinical trials [Kanatas AN, Rogers SN. A national survey of health-related quality of life questionnaires in head and neck oncology. Ann R Coll Surg Engl 2004;86:6-10.], and reviews [Kanatas AN, Rogers SN. A national survey of health-related quality of life questionnaires in head and neck oncology. Ann R Coll Surg Engl 2004;86:6-10.]. Although many facets of HRQOL following head and neck cancer have been explored over the last five years the paper identifies issues where research is still lacking.

Sub-imaging technique to improve phase only filter search capability.

A novel application of a phase only filter model, which is implementable in the optical domain, is proposed. In this application, automated target tracking is accomplished with a novel sub-imaging technique with correlation tracking inside a radius of interest. In this technique the image is subdivided and the correlation is tracked by comparing only the autocorrelation of the filter with itself. A radius of interest is used to reduce the number of computations required to track a moving target. Real-world video images are used to demonstrate the performance of the model.