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We established a volumetric trans-scale imaging system with an ultra-large field-of-view (FOV) that enables simultaneous observation of millions of cellular dynamics in centimeter-wide three-dimensional (3D) tissues and embryos. Using a custom-made giant lens system with a magnification of ×2 and a numerical aperture (NA) of 0.25, and a CMOS camera with more than 100 megapixels, we built a trans-scale scope AMATERAS-2, and realized fluorescence imaging with a transverse spatial resolution of approximately 1.1 µm across an FOV of approximately 1.5×1.0 cm 2 . The 3D resolving capability was realized through a combination of optical and computational sectioning techniques tailored for our low-power imaging system. We applied the imaging technique to 1.2 cm-wide section of mouse brain, and successfully observed various regions of the brain with sub-cellular resolution in a single FOV. We also performed time-lapse imaging of a 1-cm-wide vascular network during quail embryo development for over 24 hr, visualizing the movement of over 4.0×10 5 vascular endothelial cells and quantitatively analyzing their dynamics. Our results demonstrate the potential of this technique in accelerating production of comprehensive reference maps of all cells in organisms and tissues, which contributes to understanding developmental processes, brain functions, and pathogenesis of disease, as well as high-throughput quality check of tissues used for transplantation medicine., Competing Interests: TI, TK, YS, KI, KS, HH, HI, SO, TN No competing interests declared, YT Y.T. is an employee of SIGMAKOKI CO., LTD, SE S.E. is an employee of SIGMAKOKI CO., LTD, KS K.S. is employed part-time by LPIXEL Inc, (© 2024, Ichimura et al.)

Heterogeneity is a critical determinant for multicellular pattern formation. Although the importance of microscale and macroscale heterogeneity at the single-cell and whole-system levels, respectively, has been well accepted, the presence and functions of mesoscale heterogeneity, such as cell clusters with distinct properties, have been poorly recognized. We investigated the biological importance of mesoscale heterogeneity in signal-relaying abilities (excitability) in the self-organization of spiral waves of intercellular communications by studying the self-organized pattern formation in a population of Dictyostelium discoideum cells, a classical signal-relaying system model. By utilizing pulse-count analysis to evaluate cellular excitability, we successfully visualized the development of mesoscale heterogeneity in excitability, whose spatial scale was comparably large to that of the traveling waves of intercellular communication. Together with perturbation experiments, our detailed analysis of the structural change in mesoscale heterogeneity and associated wave dynamics demonstrated the functional importance of mesoscale heterogeneity in generating the spiral wave pattern, whose experimental observations were first realized. We propose that mesoscale heterogeneity, in addition to microscale and macroscale heterogeneities, is a critical determinant of diverse multicellular pattern formations., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

SSBD (https://ssbd.riken.jp) is a platform for the sharing and reuse of bioimaging data. As part of efforts to build a bioimaging data ecosystem, SSBD has recently been updated to a two-tiered data resource comprising SSBD:repository, a public repository for the sharing of all types of bioimaging data reported in journals, and SSBD:database, an added-value database for the sharing of curated, highly reusable, metadata-rich data. This update addresses the conflicting demands of rapid data publication and sharing of richly annotated data, thereby promoting bioimaging data sharing and reuse. With this update, SSBD is now positioned as a core repository and database within the foundingGIDE, an international consortium working to establish a global image data ecosystem. Harmonizing metadata between data resources enables cross-searching and data exchange with data resources from other countries and regions., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Zebrafish is a useful model organism in neuroscience; however, its gene expression atlas in the adult brain is not well developed. In the present study, we examined the expression of 38 neuropeptides, comparing with GABAergic and glutamatergic neuron marker genes in the adult zebrafish brain by comprehensive in situ hybridization. The results are summarized as an expression atlas in 19 coronal planes of the forebrain. Furthermore, the scanned data of all brain sections were made publicly available in the Adult Zebrafish Brain Gene Expression Database (https://ssbd.riken.jp/azebex/). Based on these data, we performed detailed comparative neuroanatomical analyses of the hypothalamus and found that several regions previously described as one nucleus in the reference zebrafish brain atlas contain two or more subregions with significantly different neuropeptide/neurotransmitter expression profiles. Subsequently, we compared the expression data in zebrafish telencephalon and hypothalamus obtained in this study with those in mice, by performing a cluster analysis. As a result, several nuclei in zebrafish and mice were clustered in close vicinity. The present expression atlas, database, and anatomical findings will contribute to future neuroscience research using zebrafish., (© 2024 The Authors. The Journal of Comparative Neurology published by Wiley Periodicals LLC.)

Summary: High-throughput chromosome conformation capture (Hi-C) is a widely used assay for studying the three-dimensional (3D) genome organization across the whole genome. Here, we present PHi-C2, a Python package supported by mathematical and biophysical polymer modeling that converts input Hi-C matrix data into the polymer model's dynamics, structural conformations and rheological features. The updated optimization algorithm for regenerating a highly similar Hi-C matrix provides a fast and accurate optimal solution compared to the previous version by eliminating the factors underlying the inefficiency of the optimization algorithm in the iterative optimization process. In addition, we have enabled a Google Colab workflow to run the algorithm, wherein users can easily change the parameters and check the results in the notebook. Overall, PHi-C2 represents a valuable tool for mining the dynamic 3D genome state embedded in Hi-C data., Availability and Implementation: PHi-C2 as the phic Python package is freely available under the GPL license and can be installed from the Python package index. The source code is available from GitHub at https://github.com/soyashinkai/PHi-C2. Moreover, users do not have to prepare a Python environment because PHi-C2 can run on Google Colab (https://bit.ly/3rlptGI)., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2022. Published by Oxford University Press.)

Neuronal birthdate is one of the major determinants of neuronal phenotypes. However, most birthdating methods are retrospective in nature, allowing very little experimental access to the classified neuronal subsets. Here, we introduce four neurogenic tagging mouse lines, which can assign CreER- loxP recombination to neuron subsets that share the same differentiation timing in living animals and enable various experimental manipulations of the classified subsets. We constructed a brain atlas of the neurogenic tagging mouse lines (NeuroGT), which includes holistic image data of the loxP -recombined neurons and their processes across the entire brain that were tagged on each single day during the neurodevelopmental period. This image database, which is open to the public, offers investigators the opportunity to find specific neurogenic tagging driver lines and the stages of tagging appropriate for their own research purposes., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)

BD5 is a new binary data format based on HDF5 (hierarchical data format version 5). It can be used for representing quantitative biological dynamics data obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) is an XML (Extensible Markup Language)-based open format that is also used to represent such data; however, it becomes difficult to access quantitative data in BDML files when the file size is large because parsing XML-based files requires large computational resources to first read the whole file sequentially into computer memory. BD5 enables fast random (i.e., direct) access to quantitative data on disk without parsing the entire file. Therefore, it allows practical reuse of data for understanding biological mechanisms underlying the dynamics., Competing Interests: The authors have declared that no competing interests exist.

Experimental observations indicate that the repulsion of particles is a factor that induces the transformation of vesicles containing multiple particles. Metropolis Monte Carlo simulations are performed with two models in which repulsive particles are enclosed inside a vesicle. The distribution of the particles and the effective bending coefficient and surface tension of the membrane are analyzed. The shape and internal structure of the vesicle containing the particles are investigated as the vesicle volume is decreased. It is revealed that the repulsive interaction between particles produces a layered structure and stiffens the membrane. When particles repulsively interact over a long range, the membrane takes on a dumbbell form.

Intrinsic clearances (CLint-HLM-total) for the metabolism of NE-100, metoprolol, clarithromycin (CAM), lornoxicam and tenoxicam were predicted from in vitro data with recombinant cytochorme P450s (CYPs) using relative activity factor (RAF) and then compared with CLint-HLM observed in human liver microsomes (HLM). The predicted CLint-HLM-total correlated well with the observed CLint-HLM in HLM. When oral clearances (CLoral) of low-clearance drugs such as metoprolol, CAM, lornoxicam and tenoxicam were predicted from the in vitro data using four physiological models (well-stirred, parallel tube, distributed and dispersion models), the predicted CLoral corresponded well with the observed CLoralin vivo and were similar among the four models. For a high-clearance drug, the predicted CLoral of NE-100 in extensive CYP2D6 metabolizers (EMs) was substantially different between individual models, although the predicted CLoral in a poor metabolizer of CYP2D6 (PMs) was similar. The CLoral ratio of NE-100 between the EMs and the PMs predicted from the dispersion model, which leads to a reliable prediction for the high-clearance drug, was 48.4, but the ratio decreased depending on the increase of the NE-100 plasma concentration. The results suggest that the CLoral decrease in the EMs is caused by saturation of NE-100 metabolism mediated by CYP2D6 and is based on increases in plasma NE-100 concentrations dependent on the dose of NE-100. The study suggests that the RAF and the in vitro-in vivo scaling approaches are useful for predicting CLoral from in vitro data with recombinant CYPs without using HLM and hepatocytes.

The human cytochrome P450 (CYP) isoforms catalyzing the oxidation metabolism of desglymidodrine (DMAE), an active metabolite of midodrine, were studied. Recombinant human CYP2D6, 1A2 and 2C19 exhibited appreciable catalytic activity with respect to the 5'-O-demethylation of DMAE. The O-demethylase activity by the recombinant CYP2D6 was much higher than that of other CYP isoforms. Quinidine (a selective inhibitor of CYP2D6) inhibited the O-demethylation of DMAE in pooled human microsomes by 86%, while selective inhibitors for other forms of CYP did not show any appreciable effect. Although the activity of CYP2D6 was almost negligible in the PM microsomes, the O-demethylase activity of DMAE was found to be maintained by about 25% of the pooled microsomes. Furafylline (a selective inhibitor of CYP1A2) inhibited the M-2 formation in the PM microsomes by 57%. The treatment of pooled microsomes with an antibody against CYP2D6 inhibited the formation of M-2 by about 75%, whereas that of the PM microsomes did not show drastic inhibition. In contrast, the antibody against CYP1A2 suppressed the activity by 40 to 50% in the PM microsomes. These findings suggest that CYP2D6 have the highest catalytic activity of DMAE 5'-O-demethylation in human liver microsomes, followed by CYP1A2 to a small extent.

Differences in the major histocompatibility complex (MHC) between recipients and donors present a problem because of immunologic responses in graft rejection. The purpose of this study is to clarify the efficacy of MHC matching against acute graft rejection of allogeneic limb transplants in rats. Right hindlimb transplantations were performed using various MHC-mismatched pairs of inbred rats. The rats were classified into 5 groups according to the differences in subregions of the RT1 (rat MHC) between the recipient and the donor: group 1, RT1-A,B,D barrier (the differences of RT1-A,B,D subregions); group 2, RT1-A barrier; group 3, RT1-B,D barrier; group 4, RT1-B barrier; and group 5, RT1-D barrier. The mean survival time significantly decreased in group 1 and increased in group 4. The results suggest that MHC matching clearly improves survival of transplanted limbs. Specifically, both RT1-A and D matching is the most effective compatibility in prolonging survival time of allogeneic limb transplants in rats.

We report five children with transverse defects of the upper limb who developed calcified deposits at the distal end of the limb. The lesions were excised from two children and had the typical histological appearance of tumoral calcinosis but on clinical grounds it is unlikely that this is the same condition as that previously described as tumoral calcinosis.

Trifluoperazine, a calmodulin antagonist, suppressed the clofibric acid-evoked induction of the peroxisomal cyanide-insensitive fatty acyl-CoA oxidizing system and carnitine acetyltransferase in rat liver and also in cultured rat hepatocytes. H-7, a potent inhibitor of protein kinase C, also suppressed the induction of these enzymes by clofibric acid, bezafibrate, Wyl4,643 or mono(2-ethylhexyl)phthalate in cultured rat hepatocytes. This suppressive effect was also confirmed by the protein composition of hepatocytes treated with clofibric acid and these antagonists, where the increase in the amount of peroxisomal bifunctional enzyme by peroxisome proliferator was markedly suppressed by above two antagonists. Profile of the time-dependent changes in the activities of the two enzymes after clofibric acid treatment showed that there might be two phases in the induction process. The initial phase (0-3 days after the treatment) showed a relative low inducing rate and subsequent phase (3-5 days after the treatment) showed an abrupt induction. The suppressive effect of the above two antagonists was significant in the later phase. In a time course study of the induction process of peroxisomal catalase, bifunctional enzyme or 69 kDa integral membrane protein using immunochemical detection, the induction of the membrane protein by clofibric acid was delayed compared with that of the bifunctional enzyme, where the induction was inhibited almost completely by nicardipine. These experimental results suggest that calmodulin- and protein kinase C-dependent processes play an important role in the process of marked induction of peroxisomal enzymes and membrane protein by drugs in rat liver.

Experience with infected pseudarthrosis with segmental osseous defect, treated by debridement and microvascular bone transfer, is reported. Fourteen patients form the basis for the study, including 12 males and two females. Patient age at the time of operation averaged 35.1 years. Follow-up averaged 52 months. The affected site included tibia (10), femur (2), and ulna (2). A total of 15 vascularized bone graft transfers were carried out for the 14 patients, with the donor bone fibula (8) and ilium (7). Bony union was ultimately obtained in all patients. In 11 patients, primary union was obtained at both ends of the transferred bone segment. In the remaining three patients, a secondary procedure, consisting of onlay nonvascularized bone autografting at one end of the vascularized transferred bone segment, was required to obtain union. Recurrent infection following union occurred in one patient. One of the two patients with active osteomyelitis at the time of vascularized bone transfer had complications from recurrent sepsis, leading to the authors' caveat that vascularized bone transfer should be deferred until such time as sepsis is inactive. Criteria used in this series for determining inactive sepsis (absence of sinus tracts, negative bacterial cultures, negative c-reactive protein, and a sedimentation rate of less than 15 mm per hour) seem appropriate. The study suggests that vascularized bone transfer is a useful procedure for the treatment of infected segmental osseous defects of long bones, of more than 3 cm extent and one month or more after inactive sepsis.

Kienbock's disease occurs most frequently between 20 and 30 years of age (Gillespie, 1961). The youngest patient with Kienbock's disease in literature written in English is a 10-year-old boy (Nakamura et al., 1990). We report the case of an 11-year-old girl with Kienbock's disease whom we treated with radial shortening. Five months after surgery, radiographs showed signs of rapid disappearance of avascular necrosis of the lunate, and the patient had excellent clinical results. Two years postoperatively no recurrence of avascular necrosis of the lunate has occurred.

Sixteen wrists of 15 patients with traumatic triangular fibrocartilage complex tears were treated by hemiresection-interposition arthroplasty of the distal radioulnar joint combined with repair of the torn triangular fibrocartilage complex. The surgical procedure was performed to avoid impingement of the ulnar head against the reconstructed triangular fibrocartilage complex. Most of the wrists showed a positive ulnar variance. The average age of the patients was 39 years. Follow-up averaged 41 months. Complete relief of pain was obtained in 10 wrists. Slight pain persisted in 6 wrists, although it was less than before surgery. The range of motion of the wrist joint and forearm improved postoperatively. Grip strength in all wrists increased. Postoperative complications occurred in 7 wrists of 6 patients: reoperation in 2 wrists, fracture in 1, and tendinitis of the extensor carpi ulnaris in 4. All 15 patients subsequently returned to their previous occupations.

The in vivo effect of nicardipine, a well-known calcium antagonist, on microsomal omega-oxidation of laurate in clofibrate-treated rat liver was studied. The 15.3-fold induction of the activity by 2 weeks administration of 0.25% clofibrate in the diet was markedly suppressed to about 6-fold by co-administration of nicardipine at 100 mg/kg body weight. Similarly, the induction of peroxisomal beta-oxidation and carnitine acetyltransferase activities were also suppressed by this simultaneous administration by more than 50%. Although clofibrate also induced the activity of reduced nicotineamide adenine dinucleotide phosphate (NADPH)-cytochrome c reductase and increased the hepatic content of cytochrome P-450, no suppressive effect of nicardipine was observed. Contrarily, nicardipine induced the reductase activity and increased the hepatic content of cytochromes P-450 and b5. These results provide the first demonstration of a calcium antagonist, e.g. nicardipine acting as inhibitor of the induction of microsomal omega-oxidation, in association with the inhibition of peroxisome proliferation in animals. The suppression of drug-induced peroxisome proliferation and microsomal omega-oxidation by the calcium antagonist may help in elucidating the causal relationship of the induction mechanisms between peroxisomal and microsomal enzymes.

The latissimus dorsi was transferred as a pedicle flap in ten patients and as a free vascular flap in ten others for extremity reconstruction. Group I comprised ten patients in whom the transfer was used solely to cover a skin or soft-tissue defect. Although there was partial necrosis of the transferred skin in one patient, the remaining nine patients obtained complete coverage without further reconstructive surgery. Group II comprised five patients in whom transfer of the latissimus dorsi was performed for active flexion or extension of the elbow or for abduction of the shoulder. Postoperatively, muscle strength obtained was classified from Grades 0 to 5 according to the muscle testing method. Three patients obtained muscle strength of Grade 3, while two obtained Grade 2. Group III comprised five patients who had brachial plexus palsy after high-dose irradiation. Coverage of the skin and soft tissue was performed after neurolysis of the brachial plexus palsy to free the tissue bed of scarred tissue. Postoperatively, sensory and motor disturbances were alleviated in four of five patients.

In vivo administration of nicardipine, a known calcium antagonist, suppressed the clofibrate-evoked induction of activities of peroxisomal enzymes, such as catalase, the peroxisomal fatty acyl-CoA oxidizing system, carnitine acetyltransferase and mitochondrial carnitine palmitoyltransferase in rat liver. On a time-course study, the suppression of induction in the activities of the peroxisomal fatty acyl-CoA oxidizing system and carnitine acetyltransferase was found at 5 days after the treatment, whereas the induction by clofibrate was already observed at 1 day after the treatment, suggesting that in the process of peroxisome induction by clofibrate there might be two steps, i.e., a triggering step and an enhancing step, and nicardipine might act as suppressor for the later step. The precursor-incorporation studies with [3H]leucine showed that the rate of the synthesis of the peroxisomal bifunctional enzyme was increased by 4.2-fold after clofibrate-treatment, whereas nicardipine suppressed this enhancement to only 2.2-fold of the control. The rate of degradation of this enzyme was not affected by any treatment. These results show that nicardipine affects the regulation mechanism of the biosynthesis of this enzyme. Nicardipine showed hardly any suppressive-effect on the hepatic peroxisomal enzyme induction observed in high-fat diet fed rat. Furthermore, the suppression of clofibrate-evoked induction of peroxisomal enzymes was observed also in mice. These interesting findings suggest that there is a difference in the mechanism of peroxisome proliferation and/or the induction of peroxisomal enzymes between clofibrate and physiological conditions, such as high-fat diet feeding. The suppression of drug-induced peroxisome proliferation by calcium antagonists may help in dissecting the causal relationship between the multiple effects mediated by peroxisomal proliferators.

The reverse-flow island flap is a relatively recent concept. We have applied this concept to the vascularized bone graft. We report a new method of the reverse-flow vascularized fibular graft for two patients with a pseudarthrosis and massive bone defect of the tibia. The peroneal artery and venae comitantes were severed proximally and elevated with the fibula while maintaining distal vascular continuity. The reverse-flow vascularized fibula was grafted to the posterior aspect of the bone defect of the tibia. Bony union was obtained in both cases. The reverse-flow vascularized fibular graft has many advantages compared with free vascularized fibular graft.

The properties of single cortical neurons responding to electrical stimulation of the tooth-pulp and to intrapulpal application of bradykinin were studied in the cat. The activities of tooth-pulp driven neurons (TPNs) were recorded from the middle and anterior parts of the coronal gyrus of the cerebral cortex. Bradykinin-sensitive tooth-pulp driven neurons (BK-TPNs) were located in layer IV of area 3b of the anterior part of the coronal gyrus. These neurons had a large cutaneous oro-facial receptive field and received a nociceptive input from the facial skin as well as from the tooth-pulp. The BK-TPNs had a higher threshold and longer latency to electrical stimulation than TPNs insensitive to bradykinin (non BK-TPNs). These findings suggest that BK-TPNs in this cortical area may be involved in sensory processing of noxious information from trigeminal regions.

Postoperative results in 21 patients with bone defects that had been treated with a free vascularized fibular graft (FVFG) were evaluated. Pathogeneses in 21 patients were bone defect or pseudarthrosis after trauma in eight, massive bone defect after resection of bone and soft tissue tumor in six, congenital pseudarthrosis of the tibia in six, and congenital arteriovenous fistula in the forearm in one patient. The follow-up ranged from 15 months to 12 years, with an average of four years and six months. At final review, 12 patients went on to primary bony union, and six additional patients obtained union following an additional conventional bone graft. Three FVFGs resulted in a non-vascularized fibular graft. However, two patients obtained union with additional bone graft. Only one patient failed to obtain bony union and eventually required an above-knee amputation. Bony union rates in congenital pseudarthrosis of the tibia treated with the FVFG were lower than those in other diseases. Variables related to the surgical procedures and other factors affecting results and complications were also evaluated.

We have carried out 13 vascularized iliac osteocutaneous flaps (VIOF) based on the deep circumflex artery (DCIA) and accompanying veins for cases with compound skin and bone defects. Ten of 13 cases obtained bony union at both ends of the iliac crest with only VIOF. Two of the remaining 3 cases obtained bony union at one end only with the VIOF but united at another end with an additional conventional bone grafting procedure. The final case, a traumatic bone defect of the tibia, failed to obtain bony union at either end of the iliac segment. In 5 of 11 patients in which an osteocutaneous flap was used, complete skin flap survival occurred. Of the remaining 6, one flap went on to complete necrosis, and five flaps were complicated by superficial or partial necrosis. The incidence of flap complications was analysed according to the size of flap. Five flaps with complete survival averaged 6.8 x 10.6 cm in size; however, five flaps with superficial or partial necrosis averaged 10.0 x 15.8 cm. These results suggest that the maximal safe skin flap dimension from the DCIA supply alone is probably 10 x 15 cm.

The input pattern and spatial distribution of tooth pulp-driven neurons (TPNs) in the cat cortex were studied by recording the unitary activities of these neurons. Stimulation was applied to the upper and lower canine and molar tooth pulps. It was possible to record activities of TPNs in the deep layers of the areas 3a and 3b of the coronal gyrus of cerebral cortex. TPNs driven by the ipsilateral tooth pulp stimulation were distributed more anteroventrally than those driven by contralateral stimulation. Cells driven by bilateral pulp stimulation were situated between these two neurons. The threshold intensity for TPNs in the area 3a was lower than that for neurons in 3b. The majority of TPNs in the area 3a of the anterior part of the coronal gyrus received inputs from low-threshold masseteric muscular afferents as well as from tooth pulp afferents. The findings suggest that TPNs in the area 3a may have a relation to orofacial motor functions.

Cortical projection areas and distribution and response characteristics of masseteric nerve-driven neurons (MDN) were studied by recording surface-evoked potentials and single neuronal activities elicited by stimulation of the contralateral masseteric nerve in cats. Neuronal activities of MDNs could be recorded in two separate cortical areas. One was located in laminae II-III of area 3b of the posterior part of the coronal gyrus (P), and the other in laminae IV-V of areas 3a and 6a beta of the anterior parts of the coronal and lateral sigmoid gyri (A). The majority of MDNs were driven by low-threshold muscle afferents (Group I and II). Peak latencies of MDNs in P were shorter than those in A. Intracortical microstimulation (less than 30 microA) in A produced oro-facial movements while stimulation in P did not produce any motor effects.

Functional properties of the jaw and orofacial motor areas in the cerebral cortex of the lightly anesthetized cat were studied on the basis of the motor effects produced by intracortical microstimulation (ICMS). Jaw and orofacial motor effects were evoked by ICMS (less than 30 microA) delivered to the anterior parts of the coronal and lateral sigmoid gyri (C, coronal area), and the anterior part of the orbital gyrus (O, orbital area). Different patterns of movements in the jaw and orofacial regions were evoked from these two areas. In C one or, at most, two types of simple movement were produced by ICMS to one location, while in O more coordinated movements than those in C were produced. Cytoarchitectonically the jaw and orofacial motor areas were restricted to areas 3a, 4 gamma, and 6a beta in C, and to area 43 in O.