Application of a novel numerical simulation to biochemical reaction systems.

Recent advancements in omics and single-cell analysis highlight the necessity of numerical methods for managing the complexity of biological data. This paper introduces a simulation program for biochemical reaction systems based on the natural number simulation (NNS) method. This novel approach ensures the equitable treatment of all molecular entities, such as DNA, proteins, H2O, and hydrogen ions (H+), in biological systems. Central to NNS is its use of stoichiometric formulas, simplifying the modeling process and facilitating efficient and accurate simulations of diverse biochemical reactions. The advantage of this method is its ability to manage all molecules uniformly, ensuring a balanced representation in simulations. Detailed in Python, NNS is adept at simulating various reactions, ranging from water ionization to Michaelis-Menten kinetics and complex gene-based systems, making it an effective tool for scientific and engineering research.

Impact of preS1 Evaluation in the Management of Chronic Hepatitis B Virus Infection.

Background and Objectives: The measurement of hepatitis B surface antigen (HBsAg) is essential for managing chronic hepatitis B virus infection (CHB). HBsAg consists of three different surface envelope proteins: large, middle, and small HB surface proteins. However, in clinical practice, it is not common to evaluate each of these HB surface proteins separately. Materials and Methods: In this study, we investigated preS1 expression using seven monoclonal antibodies (mAbs) in 68 CHB patients, as well as examining their antigenicity. Results: Although the seven mAbs had been derived from genotype (Gt) C, they could recognize preS1 with Gts A to D. The epitopes were concentrated within the aa33-47 region of preS1, and their antigenicity was significantly reduced by an aa45F substitution. We found that preS1 expression remained consistent regardless of HBsAg levels and different Gts in CHB patients, in contrast to what was observed in SHBs. Conclusions: These results suggest that the antigenic epitope is preserved among different Gts and that the expression pattern of preS1 is altered during CHB, highlighting its vital role in the HBV infection cycle. Our present results suggest preS1 is a promising therapeutic target in CHB.

Accuracy of an image matching technique for assessing knee alignment during the stance phase of gait using single-plane anteroposterior radiography.

BACKGROUND: Accurate measurement of bone alignment of the knee during walking provides ideal clinical information for diagnosis and treatment of knee joint disorders. To bring this ideal closer to clinical reality, we developed an image matching technique to measure the three-dimensional (3D) position of bones using anteroposterior radiography during the stance phase of treadmill walking. OBJECTIVE: To develop and validate an image matching method for evaluation of 3D knee alignment using anteroposterior radiography of artificial femoral and tibial bones. METHODS: The 3D position of each bone was recovered by minimizing the difference between the projected outline and the contour of the bone in the anteroposterior radiograph. The true value of the position was measured using a 3D coordinate measuring machine. RESULTS: The mean values ± standard deviation and root mean squares (RMS) of translation errors were within -1.6 ± 2.1 mm and 2.6 mm, respectively, for femur, and 2.1 ± 1.9 mm and 2.8 mm for tibia. The mean values ± standard deviation and RMS of errors in rotation were within 0.3 ± 0.7° and 0.7°, respectively, for femur, and -0.3 ± 0.9° and 0.9°, respectively, for tibia. CONCLUSION: Our method is suitable for evaluating 3D knee alignment on anteroposterior radiography.

Sex Differences in Predicting Difficult Laryngeal Exposure: Validation and Modification of Predictive Models.

OBJECTIVES/HYPOTHESIS: To determine the presence of sex differences in difficult laryngeal exposure and the Laryngoscore, validate the Laryngoscore, mini-Laryngoscore, and Clarysse's model for predicting difficult laryngeal exposure, and modify the Laryngoscore for improved prediction accuracy. STUDY DESIGN: Retrospective study. METHODS: This study included 153 patients who underwent laryngeal microsurgery at a tertiary laryngology center and university hospital. Patients were evaluated using the 11 items of the Laryngoscore, mini-Laryngoscore, and Clarysse's model to predict difficult laryngeal exposure. Difficult laryngeal exposure was defined as the inability to view the anterior commissure through a rigid laryngoscope under counterpressure to the anterior neck. Descriptive statistics and receiver-operating characteristic curve analysis were used to assess the diagnostic performance of the predictive models and variables, including sex. RESULTS: The prevalence of difficult laryngeal exposure was significantly higher in men than in women, despite higher Laryngoscore values in females. The Laryngoscore, mini-Laryngoscore, and Clarysse's model demonstrated good diagnostic performance with C-indexes of 0.751, 0.727, and 0.783, respectively. Based on these findings, we proposed a modified Laryngoscore, including treatment history, interincisors gap, upper jaw dental status, thyro-mental distance, degree of neck flexion-extension, and sex, achieving a C-index of 0.835. CONCLUSIONS: Inclusion of sex in the Laryngoscore and related predictive models enhances the accuracy of predicting difficult laryngeal exposure. These findings support the inclusion of sex as a factor in future modifications of these models to improve their predictive performance.

BayesianSpikeFusion: accelerating spiking neural network inference via Bayesian fusion of early prediction.

Spiking neural networks (SNNs) have garnered significant attention due to their notable energy efficiency. However, conventional SNNs rely on spike firing frequency to encode information, necessitating a fixed sampling time and leaving room for further optimization. This study presents a novel approach to reduce sampling time and conserve energy by extracting early prediction results from the intermediate layer of the network and integrating them with the final layer's predictions in a Bayesian fashion. Experimental evaluations conducted on image classification tasks using MNIST, CIFAR-10, and CIFAR-100 datasets demonstrate the efficacy of our proposed method when applied to VGGNets and ResNets models. Results indicate a substantial energy reduction of 38.8% in VGGNets and 48.0% in ResNets, illustrating the potential for achieving significant efficiency gains in spiking neural networks. These findings contribute to the ongoing research in enhancing the performance of SNNs, facilitating their deployment in resource-constrained environments. Our code is available on GitHub: https://github.com/hanebarla/BayesianSpikeFusion.

Ozenoxacin suppresses sebum production by inhibiting mTORC1 activation in differentiated hamster sebocytes.

Acne vulgaris is a complex condition involving factors that affect the pilosebaceous unit. A primary manifestation of acne pathology is the development of comedones, often linked to the overproduction of sebum resulting from 5α-dihydrotestosterone (5α-DHT) and insulin activity. Ozenoxacin is a topical quinolone that exhibits potent antibacterial activity against Cutibacterium acnes (C. acnes). It is commonly used to treat acne associated with this bacterium; however, its effect on sebum production within the sebaceous glands remains unclear. In this study, the effects of ozenoxacin on sebum production were examined using insulin- and 5α-DHT-differentiated hamster sebocytes. Ozenoxacin showed a dose-dependent inhibition of lipid droplet formation and triacylglycerol (TG) production, which is a major component of sebum. In addition, it suppressed the expression of diacylglycerol acyltransferase 1, stearoyl-CoA desaturase-1, and perilipin-1 mRNA, all important factors involved in sebum synthesis, in a dose-dependent manner. Moreover, ozenoxacin decreased phosphorylated 40S ribosomal protein S6 levels downstream of the mechanistic/mammalian target of rapamycin complex 1 (mTORC1), without altering the phosphorylation of Akt, an upstream regulator of mTORC1, in both insulin- and 5α-DHT-treated hamster sebocytes. Interestingly, nadifloxacin, but not clindamycin, exhibited a similar suppression of sebum production, albeit with lesser potency compared with ozenoxacin. Furthermore, a topical application of a 2% ozenoxacin-containing lotion to the auricle skin of hamsters did not affect the size of the sebaceous glands or epidermal thickness. Notably, it decreased the amount of TG on the skin surface. The results provide novel insights into the sebum-inhibitory properties of ozenoxacin, indicating its potential efficacy in controlling microbial growth and regulating sebum production for acne management.

Effects of three-dimensional femur and tibia postures on the parameters of standing long-leg radiographs for osteoarthritic knees in elderly female subjects.

BACKGROUND: Long-leg frontal radiographs of the lower extremities are used to assess knee osteoarthritis. Given the three-dimensional (3D) nature of alignment changes in osteoarthritis, postural alterations in the femur and tibia extend beyond the coronal plane (in-plane) to include the transverse and sagittal planes (out-of-plane). This study investigates the impact of these out-of-plane factors on in-plane knee alignment parameters observed in frontal radiographs. METHODS: A total of 97 osteoarthritic knees in women were examined. Using a 3D-to-two-dimensional (2D) image matching technique, we evaluated the 3D postures of the femur and tibia in the standing position as viewed from frontal radiographs in the world coordinate system. Statistical analyses were conducted to explore associations between these 3D postures and 2D alignment parameters obtained from frontal radiographs under identical conditions. FINDINGS: The femur exhibited a medial inclination of 2.7°, a posterior inclination of 3.9°, and an internal rotation of 4.2°, whereas the tibia showed a lateral inclination of 6.4°, an anterior inclination of 6.7°, and an internal rotation of 6.7°. Both coronal and rotational postures of femur and tibia influenced the hip-knee-ankle angle, mechanical axis percentage, and medial proximal tibial angle. However, only coronal factors of tibia impacted tibial joint line obliquity relative to the floor. INTERPRETATION: Attention should be paid to the potential impact of the out-of-plane postures of the femur and tibia on parameters assessed in plain frontal radiographs of the lower extremities.

Ad libitum feeding of silkworm larvae powder-containing diets specifically influences metabolism-related and short-chain fatty acid-producing gut bacteria in mice.

Silkworm (Bombyx mori) larvae are expected to be useful as an ingredient in entomophagy. They are full of nutrients, including indigestible proteins; however, there have been few studies on the effects of the consumption of the entire body of silkworms on the intestinal microflora. We prepared a customized diet containing silkworm larval powder (SLP), and investigated the effects of ad libitum feeding of the SLP diet on the intestinal microbiota and the amount of short-chain fatty acids (SCFAs) in mice. We found that the diversity of the cecal and fecal microbiota increased in the mice fed the SLP diet (SLP group), and that the composition of their intestinal microbiota differed from that of the control mice. Furthermore, a genus-level microbiota analysis showed that in the SLP group, the proportions of Alistipes, Lachnospiraceae A2, and RF39, which are associated with the prevention of obesity, were significantly increased, while the proportions of Helicobacter and Anaerotruncus, which are associated with obesity, were significantly decreased. Additionally, the level of butyrate was increased in the SLP group, and Clostridia UCG 014 and Lachnospiraceae FCS020 were found to be associated with the level of butyrate, one of the major SCFAs. These findings indicated that silkworm powder may be useful as an insect food that might also improve obesity.

Difference in the immediate effect on positional nystagmus for head positions with interval time during Epley maneuver: a randomized trial.

OBJECTIVES: The Epley maneuver (EM) shows immediate effect, wherein disappearance of positional nystagmus occurs soon after the EM. Our previous study showed that setting interval times during the EM reduced the immediate effect. The purpose of this study is to identify the head position for which interval time reduces the immediate effect. METHODS: Fifty-one patients with posterior canal type of benign paroxysmal positional vertigo (BPPV) were randomly assigned to the following three groups: 10 min interval time set at the first head position of the EM in group A, at the third head position in group B, and at the fourth head position in group C. The primary outcome measure (POï¼­) was the ratio of maximum slow-phase eye velocity of positional nystagmus soon after the EM, compared with that measured before the EM. A large ratio value indicates a poor immediate effect of the EM. RESULTS: The POï¼­ in group A (0.07) was smallest (B: 0.36, C: 0.49) (p < 0.001). DISCUSSION: The interval times at the third and fourth head positions reduced the immediate effect of the EM. Our previous study showed that the effect of BPPV fatigue is continued by maintaining the first head position of the EM. BPPV fatigue constitutes fatigability of positional nystagmus with repeated performance of the Dix-Hallpike test. Our findings may be interpreted in accordance with the theory that the immediate effect of the EM is BPPV fatigue itself, because we observed that the effect of BPPV fatigue is strongest in group A.

Alpha band modulation caused by selective attention to music enables EEG classification.

Humans are able to pay selective attention to music or speech in the presence of multiple sounds. It has been reported that in the speech domain, selective attention enhances the cross-correlation between the envelope of speech and electroencephalogram (EEG) while also affecting the spatial modulation of the alpha band. However, when multiple music pieces are performed at the same time, it is unclear how selective attention affects neural entrainment and spatial modulation. In this paper, we hypothesized that the entrainment to the attended music differs from that to the unattended music and that spatial modulation in the alpha band occurs in conjunction with attention. We conducted experiments in which we presented musical excerpts to 15 participants, each listening to two excerpts simultaneously but paying attention to one of the two. The results showed that the cross-correlation function between the EEG signal and the envelope of the unattended melody had a more prominent peak than that of the attended melody, contrary to the findings for speech. In addition, the spatial modulation in the alpha band was found with a data-driven approach called the common spatial pattern method. Classification of the EEG signal with a support vector machine identified attended melodies and achieved an accuracy of 100% for 11 of the 15 participants. These results suggest that selective attention to music suppresses entrainment to the melody and that spatial modulation of the alpha band occurs in conjunction with attention. To the best of our knowledge, this is the first report to detect attended music consisting of several types of music notes only with EEG.

Identification of Ppy-lineage cells as a novel origin of pancreatic ductal adenocarcinoma.

The Ppy gene encodes pancreatic polypeptide (PP) secreted by PP- or γ-cells, which are a subtype of endocrine cells localised mainly in the islet periphery. For a detailed characterisation of PP cells, we aimed to establish PP cell lines. To this end, we generated a mouse model harbouring the SV40 large T antigen (TAg) in the Rosa26 locus, which is expressed upon Ppy-promoter-mediated Cre-loxP recombination. Whereas Insulin1-CreERT-mediated TAg expression in beta cells resulted in insulinoma, surprisingly, Ppy-Cre-mediated TAg expression resulted in the malignant transformation of Ppy-lineage cells. These mice showed distorted islet structural integrity at 5 days of age compared with normal islets. CK19+ duct-like lesions contiguous with the islets were observed at 2 weeks of age, and mice developed aggressive pancreatic ductal adenocarcinoma (PDAC) at 4 weeks of age, suggesting that PDAC can originate from the islet/endocrine pancreas. This was unexpected as PDAC is believed to originate from the exocrine pancreas. RNA-sequencing analysis of Ppy-lineage islet cells from 7-day-old TAg+ mice showed a downregulation and an upregulation of endocrine and exocrine genes, respectively, in addition to the upregulation of genes and pathways associated with PDAC. These results suggest that the expression of an oncogene in Ppy-lineage cells induces a switch from endocrine cell fate to PDAC. Our findings demonstrate that Ppy-lineage cells may be an origin of PDAC and may provide novel insights into the pathogenesis of pancreatic cancer, as well as possible therapeutic strategies. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Vertical infantile nystagmus: Explanation of why the direction of nystagmus is vertical.

This case report presents a rare case of infantile nystagmus syndrome (INS) in which the direction of infantile nystagmus (IN) was vertical. A 66-year-old woman was referred to our department for investigation of abnormal eye movements. She showed a disordered field of view with a homonymous hemianopia in the lower left quadrant and vertical gaze-evoked nystagmus, but there were no other abnormal neurological findings. She did not complain of an oscillopsia. Imaging revealed that the cause of hemianopia was atrophy and low cerebral blood flow in the right occipital lobe. The vertical nystagmus became strong when attempting to fixate to stationary targets. A reversed optokinetic nystagmus response was observed in the vertical optokinetic nystagmus test. From these eye movements, we diagnosed her nystagmus as vertical IN. Patients with INS see everything by saccades. IN consists of the alternate appearance of saccades and preceding slow eye movements. For these eye movements, a wide visual field is necessary. In this case, vertical IN was caused by the wider vertical than horizontal visual field resulting from homonymous hemianopia. Therefore, the direction of IN is horizontal in most patients with INS because their horizontal visual field is the widest field.

Encoding of self-initiated actions in axon terminals of the mesocortical pathway.

Significance: The initiation of goal-directed actions is a complex process involving the medial prefrontal cortex and dopaminergic inputs through the mesocortical pathway. However, it is unclear what information the mesocortical pathway conveys and how it impacts action initiation. In this study, we unveiled the indispensable role of mesocortical axon terminals in encoding the execution of movements in self-initiated actions. Aim: To investigate the role of mesocortical axon terminals in encoding the execution of movements in self-initiated actions. Approach: We designed a lever-press task in which mice internally determine the timing of the press, receiving a larger reward for longer waiting periods. Results: Our study revealed that self-initiated actions depend on dopaminergic signaling mediated by D2 receptors, whereas sensory-triggered lever-press actions do not involve D2 signaling. Microprism-mediated two-photon calcium imaging further demonstrated ramping activity in mesocortical axon terminals approximately 0.5 s before the self-initiated lever press. Remarkably, the ramping patterns remained consistent whether the mice responded to cues immediately for a smaller reward or held their response for a larger reward. Conclusions: We conclude that mesocortical dopamine axon terminals encode the timing of self-initiated actions, shedding light on a crucial aspect of the intricate neural mechanisms governing goal-directed behavior.

Functional diversity of dopamine axons in prefrontal cortex during classical conditioning.

Midbrain dopamine neurons impact neural processing in the prefrontal cortex (PFC) through mesocortical projections. However, the signals conveyed by dopamine projections to the PFC remain unclear, particularly at the single-axon level. Here, we investigated dopaminergic axonal activity in the medial PFC (mPFC) during reward and aversive processing. By optimizing microprism-mediated two-photon calcium imaging of dopamine axon terminals, we found diverse activity in dopamine axons responsive to both reward and aversive stimuli. Some axons exhibited a preference for reward, while others favored aversive stimuli, and there was a strong bias for the latter at the population level. Long-term longitudinal imaging revealed that the preference was maintained in reward- and aversive-preferring axons throughout classical conditioning in which rewarding and aversive stimuli were paired with preceding auditory cues. However, as mice learned to discriminate reward or aversive cues, a cue activity preference gradually developed only in aversive-preferring axons. We inferred the trial-by-trial cue discrimination based on machine learning using anticipatory licking or facial expressions, and found that successful discrimination was accompanied by sharper selectivity for the aversive cue in aversive-preferring axons. Our findings indicate that a group of mesocortical dopamine axons encodes aversive-related signals, which are modulated by both classical conditioning across days and trial-by-trial discrimination within a day.

Disturbance in the protein landscape of cochlear perilymph in an Alzheimer's disease mouse model.

Hearing loss is a pivotal risk factor for dementia. It has recently emerged that a disruption in the intercommunication between the cochlea and brain is a key process in the initiation and progression of this disease. However, whether the cochlear properties can be influenced by pathological signals associated with dementia remains unclear. In this study, using a mouse model of Alzheimer's disease (AD), we investigated the impacts of the AD-like amyloid ß (Aß) pathology in the brain on the cochlea. Despite little detectable change in the age-related shift of the hearing threshold, we observed quantitative and qualitative alterations in the protein profile in perilymph, an extracellular fluid that fills the path of sound waves in the cochlea. Our findings highlight the potential contribution of Aß pathology in the brain to the disturbance of cochlear homeostasis.

Evaluation of the cyclic single-chain Fv antibody derived from nivolumab by biophysical analyses and in vitro cell-based bioassay.

Single-chain Fv (scFv) is a recombinant small antibody in which a polypeptide linker connects the variable regions of the light chain (VL) and the heavy chain (VH). The practical use of scFv, however, has been prevented by its tendency to aggregate due to interchain VL-VH interactions. We recently developed a cyclic scFv whose N-terminus and C-terminus were connected by protein ligation techniques. Biophysical comparisons between cyclic and linear scFv have been conducted, but cell biological evaluations remain unexplored. Here we studied the properties of cyclic and linear scFv derived from nivolumab. Biophysical studies revealed that the thermal stability was not changed but that the antigen-binding activity was approximately 3-fold higher as a result of circularization. A cell-based PD-1/PD-L1 interaction inhibitory assay revealed that the biological activity of scFv was markedly higher in the circularized form. In addition, biophysical analysis of scFv proteins incubated in the presence of serum revealed that circularization suppressed the decrease in antigen-binding activity. It could be assumed that circularization of scFv improved stability in the presence of serum, which in turn would suggest the applicability of cyclic scFv as a biopharmaceutical format.

RASopathies for Radiologists.

RASopathies are a heterogeneous group of genetic syndromes caused by germline mutations in a group of genes that encode components or regulators of the Ras/mitogen-activated protein kinase (MAPK) signaling pathway. RASopathies include neurofibromatosis type 1, Legius syndrome, Noonan syndrome, Costello syndrome, cardiofaciocutaneous syndrome, central conducting lymphatic anomaly, and capillary malformation-arteriovenous malformation syndrome. These disorders are grouped together as RASopathies based on our current understanding of the Ras/MAPK pathway. Abnormal activation of the Ras/MAPK pathway plays a major role in development of RASopathies. The individual disorders of RASopathies are rare, but collectively they are the most common genetic condition (one in 1000 newborns). Activation or dysregulation of the common Ras/MAPK pathway gives rise to overlapping clinical features of RASopathies, involving the cardiovascular, lymphatic, musculoskeletal, cutaneous, and central nervous systems. At the same time, there is much phenotypic variability in this group of disorders. Benign and malignant tumors are associated with certain disorders. Recently, many institutions have established multidisciplinary RASopathy clinics to address unique therapeutic challenges for patients with RASopathies. Medications developed for Ras/MAPK pathway-related cancer treatment may also control the clinical symptoms due to an abnormal Ras/MAPK pathway in RASopathies. Therefore, radiologists need to be aware of the concept of RASopathies to participate in multidisciplinary care. As with the clinical manifestations, imaging features of RASopathies are overlapping and at the same time diverse. As an introduction to the concept of RASopathies, the authors present major representative RASopathies, with emphasis on their imaging similarities and differences. ©RSNA, 2024 Test Your Knowledge questions for this article are available in the supplemental material.

Mobile medial pivot (lateral slide)-type total knee arthroplasty exhibited different motion patterns between under anaesthesia and weight-bearing condition.

PURPOSE: Total knee arthroplasty (TKA), which has medial pivot and mobile-bearing mechanisms, has been developed and clinically used. However, the in vivo dynamic kinematics of the mobile medial pivot-type TKA (MMPTKA) is unclear. This study analysed the in vivo kinematics of MMPTKA in weight-bearing and nonweight-bearing conditions. METHODS: The study included 10 knees that underwent primary TKA using MMPTKA. After TKA, lateral view radiographs of the knee in full extension, 90° of flexion and passive full flexion were taken under general anaesthesia in the nonweight-bearing condition. At least 6 months postoperatively, knee motion during squatting from a weight-bearing standing position was observed using a flat-panel detector and analysed using the three-dimensional-to-two-dimensional image registration technique. RESULTS: Under anaesthesia: in passive full flexion, the anteroposterior (AP) locations of the femoral component's medial and lateral distal points were 10.2 and 16.0 mm posterior, and the rotational angles of the femoral component's X-axis (FCX) and insert were 8.1° external rotation and 18.5° internal rotation to full extension, respectively. Squatting: the AP translations of the femoral component's medial and lateral most distal points were 2.2 and 6.4 mm, and the rotational angles of the FCX and insert were 5.7° and 1.6° external rotation, respectively. Significant differences were observed in the AP translation of the femoral component's medial and lateral most distal points and changes in the insert's rotational angle when comparing under anaesthesia and squatting. CONCLUSIONS: The kinematics of the insert in MMPTKA was significantly influenced by loading and muscle contraction. The femoral component exhibited substantial external rotation and posterior translation under anaesthesia, which may contribute to achieving an optimal range of motion. The insert remained relatively stable during squatting and minimal rotation was observed, indicating good stability. MMPTKA was expected to demonstrate rational kinematics by incorporating mobile and medial pivot mechanisms. LEVEL OF EVIDENCE: Level IV, prospective biomechanical case series study.