Search

Zafer Orkun Toktas,1,2 Baran Yilmaz,1 Murat Şakir Ekşi,1,3 Lei Wang,2,4 Akin Akakin,1 Yasin Yener,5 Murat Konakcı,6 Emre Ayan,7 Turker Kılıc,1 Deniz Konya,1,2 Yang D Teng2,4 1Department of Neurosurgery, Bahçeşehir University Medical Faculty, Istanbul, Turkey; 2Departments of Physical Medicine and Rehabilitation and Neurosurgery, Harvard Medical School, Boston, MA, USA; 3Department of Orthopedic Surgery, University of California at San Francisco, San Francisco, CA, USA; 4Division of Spinal Cord Injury Research, Veterans Affairs Healthcare System, Boston, MA, USA; 5Department of Anesthesiology, Göztepe Medikal Park Hospital, Istanbul, Turkey; 6Department of Anesthesiology, Bahçeşehir University Medical Faculty, Istanbul, Turkey; 7Department of Radiology, Göztepe Medical Park, Istanbul, Turkey Purpose: To date, application of intraoperative magnetic resonance imaging (ioMRI) to enhance surgical quality for spinal intramedullary neoplastic lesions has been rarely reported. Moreover, in developing countries or regions, ioMRI accessibility remains very limited. This report describes a technology design of high-field ioMRI accessible for multioperation rooms via a case presentation of an imaging-assisted surgical excision of human cervical spinal cord diffuse glioma.Patient and methods: The patient was a 44-year-old woman with symptomatic and progressive C2–5 intramedullary diffuse glioma (IDG). Our ioMRI system was designed and arranged with accessibility to multiple operation rooms, which was used to assure more complete spinal cord or brain tumor removal. The intraoperational diagnostic aspects and the system setup technical details are presented for future applications of the system in hospitals where a designated ioMRI suite is not available.Results: After a conventionally defined complete removal of C2–C5 IDG using a well-established surgical approach, ioMRI examination was able to detect residual tumor tissues that were indistinguishable under the surgical microscope. The IDG clusters were subsequently excised. The operation regimen resulted in a gross total elimination of the tumor, which enabled the patient to show very satisfactory postsurgery recovery and prognosis.Conclusion: ioMRI-assisted surgical removal of cervical spinal cord diffuse glioma should be systematically developed and applied to enhance therapeutic efficacy. The reported logistic flow of operating room tasks and imaging technical management are innovative for performing the tumor removal procedures in hospitals where designated ioMRI surgical suites do not exist. Critically, we emphasize implementation of stringent quality control measures for patient transportation safety and contamination prevention in establishing and maintaining such a system. Keywords: intraoperative imaging, spine, spinal cord, glioma, residual tumor, decompression

Icing in conditions where clouds contain both liquid and solid phase particles has attracted considerable interest in recent years due to numerous in-flight incidents including engine rollbacks in the vicinity of deep convective clouds in tropical regions. These incidents have prompted certification authorities to investigate and extend the icing conditions to include solid and mixed-phase clouds for airworthiness certification. These efforts have resulted in the amendments issued by the Federal Aviation Administration (FAA) and European Aviation Safety Agency (EASA) to the certification specifications of large aircraft, FAR-25 and CS-25, respectively. Flight tests, laboratory tests and computer simulations are among the acceptable means to show compliance with these specifications. Considerable effort has been spent worldwide in order to develop icing simulation software for liquid phase clouds in the past four decades, but until recently, most of these software did not have the capability for solid- or mixed-phase clouds. One of the aims of the High Altitude Ice Crystals (HAIC) project funded by the European Commission within Framework Program 7 is to address this shortcoming. The present study combines the models related to solid- and mixed-phase icing that is developed within HAIC with an in-house numerical tool. The tool has four modules; a flow-field solution module that uses the Hess-Smith panel method, a module for computing droplet and ice crystal trajectories and collection efficiencies using the Lagrangian approach, a thermodynamic module, and an ice accretion module that utilises the Extended Messinger Model. The numerical tool is tested against experimental test cases including liquid and mixed-phase conditions for various aerofoil and axisymmetric intake geometries. The agreement of the obtained results with experimental data is encouraging. [ABSTRACT FROM PUBLISHER]

Photodynamic therapy (PDT) is a photo chemotherapeutic strategy that is the application of photosensitizing agent and light on disease or tumor site. The aim of this study is to confirm the feasibility for femtosecond (fs) laser for aminolevulinate (ALA) mediated PDT on skin, breast and bladder cancer cells. Also the remarkable aspects of ALA mediated and laser induced PDT with respect to other literally known applications were investigated.

The effects of operating parameters for the esterification of free fatty acids with butanol in the presence of sulfuric acid were studied. Experiments were carried out at catalyst loadings of 0.5, 1, and 7 wt% relative to reaction mixture, butanol/free fatty acids mole ratios of 1, 2, and 6 and the temperatures of 358, 368, and 378 K. Increase in reaction temperature, acid to alcohol ratio, and catalyst loading is found to enhance the conversion of free fatty acid. In this study, the prediction of esterification reaction mechanism is conducted by a complex acid model. The influence of temperature on the kinetic constants was determined by fitting the results to the Arrhenius equation. The energy of activation for the forward reaction was found to be 67.9 kJ/mol. Vegetable-based esters are potential biodegradable base stocks for environmentally friendly lubricants. The basic lubrication parameters, such as acid value, viscosity, viscosity index, color, copper strip corrosion, foaming, and demulsifying properties, were tested and compared well with commercial standards. [ABSTRACT FROM PUBLISHER]

Background: Previous studies reported that old adults, relative to young adults, showed improvement of emotional stability and increased experiences of positive affects. in order to better understand the neural underpinnings behind the aging-related enhancement of positive affects, it is necessary to investigate whether old and young adults differ in the threshold of eliciting positive or negative emotional reactions. However, no studies have examined emotional reaction differences between old and young adults by manipulating the intensity of emotional stimuli to date. To clarify this issue, the present study examined the impact of aging on the brain’s susceptibility to affective pictures of varying emotional intensities.Methods: We recorded event-related potentials for highly negative (HN), mildly negative (MN) and neutral pictures in the negative experimental block; and for highly positive (HP), mildly positive (MP) and neutral pictures in the positive experimental block, when young and old adults were required to count the number of pictures, irrespective of the emotionality of the pictures. Results: Event-related potentials (ERP) results showed that LPP (Late positive potentials) amplitudes were larger for HN and MN stimuli compared to neutral stimuli in young adults, but not in old adults. By contrast, old adults displayed larger LPP amplitudes for HP and MP relative to neutral stimuli, while these effects were absent for young adults. In addition, old adults reported more frequent perception of positive stimuli and less frequent perception of negative stimuli than young adults. The post-experiment stimulus assessment showed more positive ratings of Neutral and MP stimuli, and reduced arousal ratings of HN stimuli in old compared to young adults. Conclusions: These results suggest that old adults are more resistant to the impact of negative stimuli, while they are equipped with enhanced attentional bias for positive stimuli. The implications of these results

Objectives: This study aimed to investigate the caries diagnosis performances of dental students after training with an artificial intelligence (AI) application utilizing deep learning techniques, a type of artificial neural network., Methods: A total of 1200 bitewing radiographs were obtained from the institution's database and two specialist dentists labeled the caries lesions in the images. Randomly selected 1000 images were used for training purposes and the remaining 200 radiographs were used to evaluate the caries diagnostic performance of the AI. Then, a convolutional neural network, a deep learning algorithm commonly employed to analyze visual imagery problems, called "You Only Look Once," was modified and trained to detect enamel and dentin caries lesions in the radiographs. Forty dental students were selected voluntarily and randomly divided into two groups. The pre-test results of dental caries diagnosis performances of both groups were recorded. After 1 week, group 2 students were trained using an AI application. Then, the post-test results of both groups were recorded. The labeling duration of the students was also measured and analyzed., Results: When both groups' pre-test and post-test results were evaluated, a statistically significant improvement was found for all parameters examined except precision score (p < 0.05). However, the trained group's accuracy, sensitivity, specificity, and F1 scores were significantly higher than the non-trained group in terms of post-test scores (p < 0.05). In group 2 (trained group), the post-test labeling time was considerably increased (p < 0.05)., Conclusions: The students trained by AI showed promising results in detecting caries lesions. The use of AI can also contribute to the clinical education of dental students., (© 2024 American Dental Education Association.)

Mechano-rehabilitation, also known as mechanotherapy, represents the forefront of noninvasive treatment for musculoskeletal (MSK) tissue disorders, encompassing conditions affecting tendons, cartilage, ligaments, and muscles. Recent emphasis has underscored the significance of macrophage presence in the healing of MSK tissues. However, a considerable gap still exists in comprehending how mechanical strains associated with mechanotherapy impact both the naïve and pro-inflammatory macrophage phenotypes within the three-dimensional (3D) tissue matrix, as well as whether the shift in macrophage phenotype is contingent on the mechanical strains inherent to mechanotherapy. In this study, we delineated alterations in mechano-adaptation and polarization of both naive and M1 macrophages within 3D matrices, elucidating their response to varying degrees of mechanical strain exposure (3%, 6%, and 12%). To evaluate macrophage mechano-adaptation and mechano-sensitivity within 3D collagen matrices under mechanical loading, we employed structural techniques (scanning electron microscopy, histology), quantitative morphological measures for phenotypic assessment, and genotypic methods such as quantitative real-time polymerase chain reaction. Our data reveal that the response of macrophages to mechanical loading is not only contingent on their specific sub-phenotype but also varies with the amplitude of mechanical strain. Notably, although supra-mechanical loading (12% strain) was requisite to induce a phenotypic shift in naive (M0) macrophages, as little as 3% mechanical strain proved sufficient to prompt phenotypic alterations in pro-inflammatory (M1) macrophages. These findings pave the way for leveraging the macrophage mechanome in customized and targeted applications of mechanical strain within the mechano-therapeutic framework. Considering the prevalence of MSK tissue injuries and their profound societal and economic implications, the development of well-informed and effective clinical mechanotherapy modalities for MSK tissue healing becomes an imperative endeavor. Impact statement Mechanotherapy is a primary noninvasive treatment for musculoskeletal (MSK) tissue injuries, but the effect of mechanical strain on macrophage phenotypes is not fully understood. A recent study found that macrophage response to mechanical loading is both sub-phenotype specific and amplitude-dependent, with even small strains enough to induce phenotypic changes in pro-inflammatory macrophages. These findings could pave the way for using macrophage mechanome in targeted mechanotherapy applications for better MSK tissue healing.

Regenerative Rehabilitation represents a multifaceted approach that merges mechanobiology with therapeutic intervention to harness the body's intrinsic tissue repair and regeneration capacity. This review delves into the intricate interplay between mechanical loading and cellular responses in the context of musculoskeletal tissue healing. It emphasizes the importance of understanding the phases involved in translating mechanical forces into biochemical responses at the cellular level. The review paper also covers the mechanosensitivity of macrophages, fibroblasts, and mesenchymal stem cells, which play a crucial role during regenerative rehabilitation since these cells exhibit unique mechanoresponsiveness during different stages of the tissue healing process. Understanding how mechanical loading amplitude and frequency applied during regenerative rehabilitation influences macrophage polarization, fibroblast-to-myofibroblast transition (FMT), and mesenchymal stem cell differentiation is crucial for developing effective therapies for musculoskeletal tissues. In conclusion, this review underscores the significance of mechanome-guided strategies in regenerative rehabilitation. By exploring the mechanosensitivity of different cell types and their responses to mechanical loading, this field offers promising avenues for accelerating tissue healing and functional recovery, ultimately enhancing the quality of life for individuals with musculoskeletal injuries and degenerative diseases., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Objectives: The aim of this study was automatically detecting and numbering teeth in digital bitewing radiographs obtained from patients, and evaluating the diagnostic efficiency of decayed teeth in real time, using deep learning algorithms., Methods: The dataset consisted of 1170 anonymized digital bitewing radiographs randomly obtained from faculty archives. After image evaluation and labeling process, the dataset was split into training and test datasets. This study proposed an end-to-end pipeline architecture consisting of three stages for matching tooth numbers and caries lesions to enhance treatment outcomes and prevent potential issues. Initially, a pre-trained convolutional neural network (CNN) utilized to determine the side of the bitewing images. Then, an improved CNN model YOLOv7 was proposed for tooth numbering and caries detection. In the final stage, our developed algorithm assessed which teeth have caries by comparing the numbered teeth with the detected caries, using the intersection over union value for the matching process., Results: According to test results, the recall, precision, and F1-score values were 0.994, 0.987 and 0.99 for teeth detection, 0.974, 0.985 and 0.979 for teeth numbering, and 0.833, 0.866 and 0.822 for caries detection, respectively. For teeth numbering and caries detection matching performance; the accuracy, recall, specificity, precision and F1-Score values were 0.934, 0.834, 0.961, 0.851 and 0.842, respectively., Conclusions: The proposed model exhibited good achievement, highlighting the potential use of CNNs for tooth detection, numbering, and caries detection, concurrently., Clinical Significance: CNNs can provide valuable support to clinicians by automating the detection and numbering of teeth, as well as the detection of caries on bitewing radiographs. By enhancing overall performance, these algorithms have the capacity to efficiently save time and play a significant role in the assessment process., (© 2024. The Author(s).)

Airborne particulate matter is one of the air pollutants which can have detrimental health effects in the human body. Radionuclides adsorb onto air particles and make their way to humans primarily through inhalation. Naturally-occurring radionuclides, 210 Pb and 210 Po, are of notable health concern due to their relatively elevated ingestion and inhalation doses. In the current study, activity concentrations of 7 Be, 210 Pb and 210 Po were determined in air particulate matter (PM). PM 2.5 was collected on the European side, while PM 10 was collected on the Anatolian side of Istanbul. Be-7, 210 Pb and 210 Po activities were found to be 5.17 ± 2.35, 0.96 ± 0.42; 0.25 ± 0.14 mBq m - 3 in Anatolian side, respectively. Be-7, 210 Pb and 210 Po activities were found to be 3.81 ± 2.27, 0.62 ± 0.29, 0.29 ± 0.26, mBq m - 3 in European side, respectively. The ratio of 210 Po/ 210 Pb was found to be higher (0.47 ± 0.31 for PM 2.5 and 0.34 ± 0.27 for PM 10 ) than the global average of 0.1. This result can be explained by the fact that Po is more volatile than Pb and enhanced in the air by the combustion process. Inhalation dose rates of 210 Pb and 210 Po due to PM 10 exposure were calculated to be 7.70 ± 3.30 and 4.05 ± 2.31 µSv year - 1 , respectively. Pb-210 bioaccessibility was assessed by the extraction of the particles in simulated lung fluids. Approximately 24.8% of inhaled 210 Pb was estimated to be bioaccessible. This study suggests that 210 Po and 210 Pb activities are partially enhanced in the air particles in Istanbul and should be regularly monitored., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Investigating macrophage plasticity emerges as a promising strategy for promoting tissue regeneration and can be exploited by regulating the transient receptor potential vanilloid 4 (TRPV4) channel. The TRPV4 channel responds to various stimuli including mechanical, chemical, and selective pharmacological compounds. It is well documented that treating cells such as epithelial cells and fibroblasts with a TRPV4 agonist enhances the Ca 2+ influx to the cells, which leads to secretion of pro-inflammatory cytokines, while a TRPV4 antagonist reduces both Ca 2+ influx and pro-inflammatory cytokine secretion. In this work, we investigated the effect of selective TRPV4 modulator compounds on U937-differentiated macrophages encapsulated within three-dimensional (3D) matrices. Despite offering a more physiologically relevant model than 2D cultures, pharmacological treatment of macrophages within 3D collagen matrices is largely overlooked in the literature. In this study, pro-inflammatory macrophages were treated with an agonist, 500 nM of GSK1016790A (TRPV4(+)), and an antagonist, 10 mM of RN-1734 (TRPV4(-)), to elucidate the modulation of the TRPV4 channel at both cellular and extracellular levels. To evaluate macrophage phenotypic alterations within 3D collagen matrices following TRPV4 modulator treatment, we employed structural techniques (SEM, Masson's trichrome, and collagen hybridizing peptide (CHP) staining), quantitative morphological measures for phenotypic assessment, and genotypic methods such as quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC). Our data reveal that pharmacological modulation of the macrophage TRPV4 channel alters the cytoskeletal structure of macrophages and influences the 3D structure encapsulating them. Moreover, we proved that treating macrophages with a TRPV4 agonist and antagonist enhances the expression of pro- and anti-inflammatory genes, respectively, leading to the upregulation of surface markers CD80 and CD206. In the TRPV4(-) group, the CD206 gene and CD206 surface marker were significantly upregulated by 9- and 2.5-fold, respectively, compared to the control group. These findings demonstrate that TRPV4 modulation can be utilized to shift macrophage phenotype within the 3D matrix toward a desired state. This is an innovative approach to addressing inflammation in musculoskeletal tissues.

In periodontitis, the bone remodeling process is disrupted by the prevalent involvement of bacteria-induced proinflammatory macrophage cells and their interaction with osteoblast cells residing within the infected bone tissue. The complex interaction between the cells needs to be deciphered to understand the dominant player in tipping the balance from osteogenesis to osteoclastogenesis. Yet, only a few studies have examined the crosstalk interaction between osteoblasts and macrophages using biomimetic three-dimensional (3D) tissue-like matrices. In this study, we created a cell-laden 3D tissue analog to study indirect crosstalk between these two cell types and their direct synergistic effect when cultured on a 3D scaffold. The cell-specific role of osteoclast differentiation was investigated through osteoblast- and proinflammatory macrophage-specific feedback studies. The results suggested that when macrophages were exposed to osteoblasts-derived conditioned media from the mineralized matrix, the M1 macrophages tended to maintain their proinflammatory phenotype. Further, when osteoblasts were exposed to secretions from proinflammatory macrophages, they demonstrated elevated receptor activator of nuclear factor-κB ligand (RANKL) expression and decreased alkaline phosphate (ALP) activities compared to osteoblasts exposed to only osteogenic media. In addition, the upregulation of tumor necrosis factor-alpha (TNF-α) and c-Fos in proinflammatory macrophages within the 3D matrix indirectly increased the RANKL expression and reduced the ALP activity of osteoblasts, promoting osteoclastogenesis. The contact coculturing with osteoblast and proinflammatory macrophages within the 3D matrix demonstrated that the proinflammatory markers (TNF-α and interleukin-1β) expressions were upregulated. In contrast, anti-inflammatory markers (c-c motif chemokine ligand 18 [CCL18]) were downregulated, and osteoclastogenic markers (TNF receptor associated factor 6 [TRAF6] and acid phosphatase 5, tartrate resistant [ACP5]) were unchanged. The data suggested that the osteoblasts curbed the osteoclastogenic differentiation of macrophages while macrophages still preserved their proinflammatory lineages. The osteoblast within the 3D coculture demonstrated increased ALP activity and did not express RANKL significantly different than the osteoblast cultured within a 3D collagen matrix without macrophages. Contact coculturing has an anabolic effect on bone tissue in a bacteria-derived inflammatory environment.

This study aimed to understand extracellular mechanical stimuli's effect on prostate cancer cells' metastatic progression within a three-dimensional (3D) bone-like microenvironment. In this study, a mechanical loading platform, EQUicycler, has been employed to create physiologically relevant static and cyclic mechanical stimuli to a prostate cancer cell (PC-3)-embedded 3D tissue matrix. Three mechanical stimuli conditions were applied: control (no loading), cyclic (1% strain at 1 Hz), and static mechanical stimuli (1% strain). The changes in prostate cancer cells' cytoskeletal reorganization, polarity (elongation index), proliferation, expression level of N-Cadherin (metastasis-associated gene), and migratory potential within the 3D collagen structures were assessed upon mechanical stimuli. The results have shown that static mechanical stimuli increased the metastasis progression factors, including cell elongation ( p < 0.001), cellular F-actin accumulation ( p < 0.001), actin polymerization ( p < 0.001), N-Cadherin gene expression, and invasion capacity of PC-3 cells within a bone-like microenvironment compared to its cyclic and control loading counterparts. This study established a novel system for studying metastatic cancer cells within bone and enables the creation of biomimetic in vitro models for cancer research and mechanobiology.

Alzheimer's Disease (AD) is a progressively debilitating form of dementia that affects millions of individuals worldwide. Although a vast amount of research has investigated the complex interplay between gut microbiota and neurodegeneration, the metaproteomic effects of microbiota on AD pathogenesis remain largely uncharted territory. This study aims to reveal the role of gut microbiota in AD pathogenesis, particularly regarding changes in the proteome and molecular pathways that are intricately linked to disease progression. We operated state-of-the-art Nano-Liquid Chromatography Mass Spectrometry (nLC-MS/MS) to compare the metaproteomic shifts of 3-month-old transgenic (3M-ALZ) and control (3M-ALM, Alzheimer's Littermate) mice, depicting the early onset of AD with those of 12-month-old ALZ and ALM mice displaying the late stage of AD. Combined with computational analysis, the outcomes of the gut-brain axis-focused inquiry furnish priceless knowledge regarding the intersection of gut microbiota and AD. Accordingly, our data indicate that the microbiota, proteome, and molecular changes in the intestine arise long before the manifestation of disease symptoms. Moreover, disparities exist between the normal-aged flora and the gut microbiota of late-stage AD mice, underscoring that the identified vital phyla, proteins, and pathways hold immense potential as markers for the early and late stages of AD. Our research endeavors to offer a comprehensive inquiry into the intricate interplay between gut microbiota and Alzheimer's Disease utilizing metaproteomic approaches, which have not been widely adopted in this domain. This highlights the exigency for further scientific exploration to elucidate the underlying mechanisms that govern this complex and multifaceted linkage.

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage., (© 2023. The Author(s).)

The rotator cuff and Achilles tendons along with the anterior cruciate ligament (ACL) are frequently injured with limited healing capacity. At the soft-hard tissue interface, enthesis is prone to get damaged and its regeneration in osteochondral defects is essential for complete healing. The current clinical techniques used in suturing procedures to reattach tendons to bones need much improvement for the generation of the native interface tissue, that is, enthesis, for patients to regain their full functions. Recently, inspired by the composite native tissue, much effort has been made to fabricate composite scaffolds for enthesis tissue regeneration. This review first focuses on the studies that used composite scaffolds for the regeneration of enthesis. Then, the use of polysaccharides for osteochondral tissue engineering is reviewed and their potential for enthesis regeneration is presented based on their supporting effects on osteogenesis and chondrogenesis. Gellan gum (GG) is selected and reviewed as a promising polysaccharide due to its unique osteogenic and chondrogenic activities that help avoid the inherent weakness of dissimilar materials in composite scaffolds. In addition, original preliminary results showed that GG supports collagen type I production and upregulation of osteogenic marker genes. Impact Statement Enthesis regeneration is essential for complete and functional healing of tendon and ligament tissues. Current suturing techniques to reattach the tendon/ligament to bones have high failure rates. This review highlights the studies on biomimetic scaffolds aimed to regenerate enthesis. In addition, the potential of using polysaccharides to regenerate enthesis is discussed based on their ability to regenerate osteochondral tissues. Gellan gum is presented as a promising biopolymer that can be modified to simultaneously support bone and cartilage regeneration by providing structural continuity for the scaffold.

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis., (© TÜBİTAK.)

Insulin is an essential factor for mammalian organisms: a regulator of glucose metabolism and other key signaling pathways. Insulin is also a multifunctional hormone whose absence can cause many diseases. Recombinant insulin is widely used in the treatment of diabetes. Understanding insulin, biosimilars, and biobetters from a holistic perspective will help pharmacologically user-friendly molecules design and develop personalized medicine-oriented therapeutic strategies for diabetes. Additionally, it helps to understand the underlying mechanism of other insulindependent metabolic disorders. The purpose of this atlas is to review insulin from a biotechnological, basic science, and clinical perspective, explain nearly all insulin-related disorders and their underlying molecular mechanisms, explore exogenous/recombinant production strategies of patented and research-level insulin/analogs, and highlight their mechanism of action from a structural perspective. Combined with computational analysis, comparisons of insulin and analogs also provide novel information about the structural dynamics of insulin., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Aim: To investigate the effect of fluid resuscitation and L-arginine administration on oxidant status markers, blood gases, lactate and apoptosis in the brain tissue of a rat model of TBI with hemorrhagic shock., Material and Methods: A total of 60 rats were divided into six groups: control, isotonic saline-treated, 7.5% NaCl-treated (hypertonic saline), L-arginine-treated (100 mg/kg), saline + L-arginine-treated and 7.5% NaCl + L-arginine-treated groups. Closed head contusive weight-drop injuries were performed with hemorrhagic shock in all of the groups. Mean arterial pressure (MAP), pulse rate, lactate, malondialdehyde (MDA), total antioxidant capacity (TAC) and apoptosis were investigated., Results: In a total of 48 rats, MAP levels remained higher than 60 mmHg for 3 hours in all of the treatment groups. The highest MAP values in each group were recorded. Higher MDA and lower TAC levels were observed in the control group than in all of the treatment groups (all p < 0.05). The number of apoptotic cells was highest in the control group and lowest in the L-arginine group., Conclusion: L-arginine administration may be an alternative treatment option for individualized fluid resuscitation in patients with TBI and hemorrhagic shock.

Lower back pain commonly arises from intervertebral disc (IVD) failure, often caused by deteriorating annulus fibrosus (AF) and/or nucleus pulposus (NP) tissue. High socioeconomic cost, quality of life issues, and unsatisfactory surgical options motivate the rapid development of non-invasive, regenerative repair strategies for lower back pain. This study aims to evaluate the AF regenerative capacity of injectable matrix repair strategy in ex vivo porcine organ culturing using collagen type-I and polycaprolactone nanofibers (PNCOL) with encapsulated fibroblast cells. Upon 14 days organ culturing, the porcine IVDs were assessed using gross optical imaging, magnetic resonance imaging (MRI), histological analysis, and Reverse Transcriptase quantitative PCR (RT-qPCR) to determine the regenerative capabilities of the PNCOL matrix at the AF injury. PNCOL-treated AF defects demonstrated a full recovery with increased gene expressions of AF extracellular matrix markers, including Collagen-I, Aggrecan, Scleraxis, and Tenascin, along with anti-inflammatory markers such as CD206 and IL10. The PNCOL treatment effectively regenerates the AF tissue at the injury site contributing to decreased herniation risk and improved surgical outcomes, thus providing effective non-invasive strategies for treating IVD injuries.

The HIV-1 Gag protein binds to the host cell membrane and assembles into immature particles. Then, in the course of immature virion budding, activated protease cleaves Gag into its main components: MA, CA, NC, and p6 proteins. The highly basic residues of MA predominantly interact with the acidic head of phosphatidyl-inositol-4,5-bisphosphate (PI(4,5)P2) inserted into the membrane. Our research group developed L-Heptanoylphosphatidyl Inositol Pentakisphosphate (L-HIPPO) and previously confirmed that this compound bound to the MA more strongly than PI(4,5)P2 and inositol hexakisphosphate (IP6) did. Therefore, herein we rationally designed eight new L-HIPPO derivatives based on the fact that the most changeable parts of L-HIPPO were two acyl chains. After that, we employed molecular docking for eight compounds via Maestro software using high-resolution crystal structures of MA in complex with IP6 (PDB IDs: 7E1I, 7E1J, and 7E1K), which were recently elucidated by our research group. The most promising docking scores were obtained with benzene-inserted compounds. Thus, we generated a library containing 213 new aromatic group-inserted L-HIPPO derivatives and performed the same molecular docking procedure. According to the results, we determined the nine new L-HIPPO derivatives most effectively binding to the MA with the most favorable scoring functions and pharmacokinetic properties for further exploration.

The spatiotemporal interaction and constant iterative feedback between fibroblasts, extracellular matrix, and environmental cues are central for investigating the fibroblast-induced musculoskeletal tissue regeneration and fibroblast-to-myofibroblast transition (FMT). In this study, we created a fibroblast-laden 3D tissue analogue to study (1) how mechanical loading exerted on three-dimensional (3D) tissues affected the residing fibroblast phenotype and (2) to identify the ideal mechanical strain amplitude for promoting tissue regeneration without initiating myofibroblast differentiation. We applied uniaxial tensile strain (0, 4, 8, and 12%) to the cell-laden 3D tissue analogues to understand the interrelation between the degree of applied mechanical loading amplitudes and FMT. Our data demonstrated that 4% mechanical strain created an anabolic effect toward tissue regeneration, but higher strain amplitudes over-stimulated the cells and initiated fibrotic tissue formation. Under increased mechanical strain amplitudes, fibroblasts were activated from a homeostatic state to a proto-myofibroblast state which resulted in increased cellularity accompanied by increased expressions of extracellular matrix (ECM) components, activation stressors (TGF-β1 and TGF-βR1), and profibrotic markers. This further transformed fibroblasts into α-smooth muscle actin expressing myofibroblasts. Understanding the interplay between the applied degree of mechanical loading exerted on 3D tissues and residing fibroblast phenotypic response is important to identify specific mechanomodulatory approaches for tissue regeneration and the informed mechanotherapy-guided tissue healing strategies., (© 2022. The Author(s).)

Study Design: Porcine intervertebral discs (IVDs) were excised and then drilled to simulate degeneration before being electrically stimulated for 21 days while undergoing mechanical loading. The discs were then analyzed for gene expression and morphology to assess regeneration., Objective: The purpose of this study was to investigate the effectiveness of the electrical stimulation of IVD treatment as an early intervention method in halting the progression of degenerative disc disease using an ex-vivo porcine model., Summary of Background Data: Treatments for degenerative disc disease are limited in their efficacy and tend to treat the symptoms of the disease rather than repairing the degenerated disc itself. There is a dire need for an early intervention treatment that not only halts the progression of the disease but contributes to reviving the degenerated disc., Methods: Lumbar IVDs were extracted from a mature pig within 1 hour of death and were drilled with a 1.5 mm bit to simulate degenerative disc disease. Four IVDs at a time were then cultured in a dynamic bioreactor system under mechanical loading for 21 days, two with and two without the electrical stimulation treatment. The IVDs were assessed using histological analysis, magnetic resonance imaging, and quantitative reverse transcriptase polymerase chain reaction to quantify the effectiveness of the treatment on the degenerated discs., Results: IVDs with electrical stimulation treatment exhibited extensive annular regeneration and prevented herniation of the nucleus pulposus (NP). In contrast, the untreated group of IVDs were unable to maintain tissue integrity and exhibited NP herniation through multiple layers of the annulus fibrosus. Gene expression showed an increase of extracellular matrix markers and antiinflammatory cytokine interleukin-4 (IL-4), while decreasing in pro-inflammatory markers and pain markers in electrically stimulated IVDs when compared to the untreated group., Conclusion: The direct electrical stimulation application in NP of damaged IVDs can be a viable option to regenerate damaged NP and annulus fibrosus tissues., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography. For complete details on the use and execution of this protocol, please refer to Durdagi et al. (2021)., Competing Interests: The authors declare no competing interests., (© 2022.)

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature., (© 2022. The Author(s).)

Objectives: This study aimed to investigate the effectiveness of deep convolutional neural network (CNN) in the diagnosis of interproximal caries lesions in digital bitewing radiographs., Methods and Materials: A total of 1,000 digital bitewing radiographs were randomly selected from the database. Of these, 800 were augmented and annotated as "decay" by two experienced dentists using a labeling tool developed in Python programming language. The 800 radiographs were consisted of 11,521 approximal surfaces of which 1,847 were decayed (lesion prevalence for train data was 16.03%). A CNN model known as you only look once (YOLO) was modified and trained to detect caries lesions in bitewing radiographs. After using the other 200 radiographs to test the effectiveness of the proposed CNN model, the accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC) were calculated., Results: The lesion prevalence for test data was 13.89%. The overall accuracy of the CNN model was 94.59% (94.19% for premolars, 94.97% for molars), sensitivity was 72.26% (75.51% for premolars, 68.71% for molars), specificity was 98.19% (97.43% for premolars, 98.91% for molars), PPV was 86.58% (83.61% for premolars, 90.44% for molars), and NPV was 95.64% (95.82% for premolars, 95.47% for molars). The overall AUC was measured as 87.19%., Conclusions: The proposed CNN model showed good performance with high accuracy scores demonstrating that it could be used in the diagnosis of caries lesions in bitewing radiographs., Clinical Significance: Correct diagnosis of dental caries is essential for a correct treatment procedure. CNNs can assist dentists in diagnosing approximal caries lesions in bitewing radiographs., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Pneumonia is a fatal disease that appears in the lungs and is caused by viral or bacterial infection. Diagnosis of pneumonia in chest X-ray images can be difficult and error-prone because of its similarity with other infections in the lungs. The aim of this study is to develop a computer-aided pneumonia detection system to facilitate the diagnosis decision process. Therefore, a convolutional neural network (CNN) ensemble method was proposed for the automatic diagnosis of pneumonia which is seen in children. In this context, seven well-known CNN models (VGG-16, VGG-19, ResNet-50, Inception-V3, Xception, MobileNet, and SqueezeNet) pre-trained on the ImageNet dataset were trained with the appropriate transfer learning and fine-tuning strategies on the chest X-ray dataset. Among the seven different models, the three most successful ones were selected for the ensemble method. The final results were obtained by combining the predictions of CNN models with the ensemble method during the test. In addition, a CNN model was trained from scratch, and the results of this model were compared with the proposed ensemble method. The proposed ensemble method achieved remarkable results with an AUC of 95.21 and a sensitivity of 97.76 on the test data. Also, the proposed ensemble method achieved classification accuracy of 90.71 in chest X-ray images as normal, viral pneumonia, and bacterial pneumonia., Competing Interests: Conflict of interestAuthors declare no conflict of interest., (© King Fahd University of Petroleum & Minerals 2021.)

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO 2 fixation cycles discovered thus far. The protein encoded by Nmar&#95;1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3-hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar&#95;1308 reduces the total number of enzymes necessary for CO 2 fixation in Thaumarchaeota, reducing the overall cost for biosynthesis. Here, we present the first high-resolution crystal structure of this bifunctional enzyme with key catalytic residues in the thaumarchaeal 3HP/4HB pathway., (© 2021. The Author(s).)

Of the most prevalent issues surrounding long-term spaceflight, the sustainability of human life and the maintenance of homeostasis in an extreme environment are of utmost concern. It has been observed that the human immune system is dysregulated in space as a result of gravitational unloading at the cellular level, leading to potential complications in astronaut health. A plethora of studies demonstrate intracellular changes that occur due to microgravity; however, these ultimately fall short of identifying the underlying mechanisms and dysfunctions that cause such changes. This comprehensive review covers the changes in human adaptive immunity due to microgravity. Specifically, there is a focus on uncovering the gravisensitive steps in T cell signaling pathways. Changes in gravitational force may lead to interrupted immune signaling cascades at specific junctions, particularly membrane and surface receptor-proximal molecules. Holistically studying the interplay of signaling with morphological changes in cytoskeleton and other cell components may yield answers to what in the T cell specifically experiences the consequences of microgravity. Fully understanding the nature of this problem is essential in order to develop proper countermeasures before long-term space flight is conducted.

Oligomerization of Pr55 Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55 Gag . However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55 Gag to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18-33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles' membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain's 2D layers during assembly and budding., (© 2021. The Author(s).)

The paracrine and autocrine processes of the host response play an integral role in the success of scaffold-based tissue regeneration. Recently, the immunomodulatory scaffolds have received huge attention for modulating inflammation around the host tissue through releasing anti-inflammatory cytokine. However, controlling the inflammation and providing a sustained release of anti-inflammatory cytokine from the scaffold in the digestive inflammatory environment are predicated upon a comprehensive understanding of three fundamental questions. (1) How does the release rate of cytokine from the scaffold change in the digestive inflammatory environment? (2) Can we prevent the premature scaffold degradation and burst release of the loaded cytokine in the digestive inflammatory environment? (3) How does the scaffold degradation prevention technique affect the immunomodulatory capacity of the scaffold? This study investigated the impacts of the digestive inflammatory environment on scaffold degradation and how pre-mature degradation can be prevented using genipin crosslinking and how genipin crosslinking affects the interleukin-4 (IL-4) release from the scaffold and differentiation of naïve macrophages (M0). Our results demonstrated that the digestive inflammatory environment (DIE) attenuates protein retention within the scaffold. Over 14 days, the encapsulated protein released 46% more in DIE than in phosphate buffer saline (PBS), which was improved through genipin crosslinking. We have identified the 0.5 ( w / v ) genipin concentration as an optimal concentration for improved IL-4 released from the scaffold, cell viability, mechanical strength, and scaffold porosity, and immunomodulation studies. The IL-4 released from the injectable scaffold could differentiate naïve macrophages to an anti-inflammatory (M2) lineage; however, upon genipin crosslinking, the immunomodulatory capacity of the scaffold diminished significantly, and pro-inflammatory markers were expressed dominantly.

Since the early 2000s, there has been a long-term price increase trend in the Istanbul housing market, and this situation also has led to price bubble speculations. Since the housing sector was caught with a high level of unsold housing stock to the economic slowdown emerging in the second half of 2018, housing price bubble speculations have increased even more, especially for the Istanbul market. In this period, housing loan interest reduction campaigns were implemented by the government through state banks to stimulate the housing demand, and a probable collapse in the housing market was prevented. On the other hand, house prices continued to rise during this period due to the stimulated demand. In this paper, we perform a price bubble research on the selected districts in the Istanbul housing market over the 2007-2019 period using LSTM autoencoder model. The first analysis on monthly data is performed by using housing price index, housing rent index, consumer prices index, stock market index, return on government debt securities, USD/TRY exchange rates, BIST price index, monthly deposit interest rates, mortgage interest rates and consumer confidence index, and the second analysis on quarterly data is carried out by adding building construction cost index and GDP data to the previous dataset. In the first analysis, the bubble formations differ regionally and periodically and disappeared toward the end of 2019 in some districts, while in the second analysis, the housing bubble formations have a more common and continuous appearance. Experimental results show that LSTM autoencoder model can be used to detect housing bubbles effectively., Competing Interests: Conflict of interestThe authors declare that they have no conflict of interest., (© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021.)

Objectives: To evaluate the role of 18 F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) for the diagnosis of anterior mediastinal masses., Methods: The oncological 18 F-FDG PET/CT images of 41 patients (17 women, 24 men; age: 16-83 years, mean age: 50.5±19.5 years) who attended the nuclear medicine department between November 2016 and September 2017 were retrospectively evaluated for the metabolic characterization of their anterior mediastinal masses., Results: Based on our results, the lesions of 4 patients were benign [maximum standard uptake value (SUV max ) <3] and that of 2 patients were non-tumoral (i.e., tuberculosis and sarcoidosis). The mean dimensions and the SUV max levels of the malignant lesions were 6.4±3.7 cm and 11.9±9.6, respectively. The pathological results for the malign tumors were thymus tumors (n=8), lymphoma (n=8), lung cancer (n=11), carcinoid metastasis (n=2), thyroid carcinoma (n=2), germ cell carcinoma (n=1), schwannoma (n=1), and sarcoma (n=1). The degree of 18 F-FDG accumulation could precisely identify the malign and benign tumors., Conclusion: Thus, contrary to the known causes, it is possible that anterior mediastinal masses originate from structures other than the anterior mediastinal structures. In this study, the lymphoma and lung carcinoma pathology were more frequent than thymic lesions.