SemiSynBio: A new era for neuromorphic computing.

Neuromorphic computing has the potential to achieve the requirements of the next-generation artificial intelligence (AI) systems, due to its advantages of adaptive learning and parallel computing. Meanwhile, biocomputing has seen ongoing development with the rise of synthetic biology, becoming the driving force for new generation semiconductor synthetic biology (SemiSynBio) technologies. DNA-based biomolecules could potentially perform the functions of Boolean operators as logic gates and be used to construct artificial neural networks (ANNs), providing the possibility of executing neuromorphic computing at the molecular level. Herein, we briefly outline the principles of neuromorphic computing, describe the advances in DNA computing with a focus on synthetic neuromorphic computing, and summarize the major challenges and prospects for synthetic neuromorphic computing. We believe that constructing such synthetic neuromorphic circuits will be an important step toward realizing neuromorphic computing, which would be of widespread use in biocomputing, DNA storage, information security, and national defense.

AIDMAN: An AI-based object detection system for malaria diagnosis from smartphone thin-blood-smear images.

Malaria is a significant public health concern, with ∼95% of cases occurring in Africa, but accurate and timely diagnosis is problematic in remote and low-income areas. Here, we developed an artificial intelligence-based object detection system for malaria diagnosis (AIDMAN). In this system, the YOLOv5 model is used to detect cells in a thin blood smear. An attentional aligner model (AAM) is then applied for cellular classification that consists of multi-scale features, a local context aligner, and multi-scale attention. Finally, a convolutional neural network classifier is applied for diagnosis using blood-smear images, reducing interference caused by false positive cells. The results demonstrate that AIDMAN handles interference well, with a diagnostic accuracy of 98.62% for cells and 97% for blood-smear images. The prospective clinical validation accuracy of 98.44% is comparable to that of microscopists. AIDMAN shows clinically acceptable detection of malaria parasites and could aid malaria diagnosis, especially in areas lacking experienced parasitologists and equipment.

Bone marrow mesenchymal stem cells-derived exosomes mediated delivery of tetramethylpyrazine attenuate cerebral ischemic injury.

OBJECTIVES: Tetramethylpyrazine (TEP) can protect the brain from ischemic damage, but it has defects such as short half-life, fast absorption, wide distribution, and rapid elimination, which limits its application. Exosomes (Exos) have the property of loading drugs and transporting signal substances. Here, we elucidated the effect of TEP-loaded bone marrow mesenchymal stem cell (BMSC)-derived Exos (Exo-TEP) on cerebral ischemic injury. MATERIALS AND METHODS: The Exos were extracted by ultracentrifugation and TEP was loaded into the Exos by electroporation. Oxygen-glucose deprivation (OGD) induced-primary cortical neurons and middle cerebral artery occlusion (MCAO)-induced mouse models were used to determine the effect of Exo-TEP on cerebral ischemic injury in vitro and in vivo. RESULTS: Exo-TEP exhibited a stable and sustained release pattern compared to free TEP. Exo-TEP treatment was more significant in improving OGD-mediated decrease in cell activity, as well as a elevation in apoptosis and ROS production in cortical neurons. In comparison with Exo and free TEP treatment, Exo-TEP treatment significantly improved pathological changes, shrunk cerebral infarction volume, as well reduced neurological deficit scores and neuronal apoptosis, and oxidative stress. CONCLUSIONS: Exo-TEP was superior to free TEP in improving cerebral ischemic injury by reducing neuronal apoptosis and oxidative stress.

Factors affecting long-term outcome in dorsal root entry zone lesioning for brachial plexus avulsion.

ABSTRACT: Dorsal root entry zone (DREZ) lesioning is a classical and effective treatment for brachial plexus avulsion (BPA). However, because of a limited number of cases reported in the literature, the factors affecting surgical outcomes are not known. Furthermore, whether this ablative procedure in the spinal level can change the status of phantom limb pain (PLP) and phantom limb sensation (PLS) is unknown. We retrospectively reviewed the patients with preganglionic BPA who underwent DREZ lesioning at a single center. Patients' baseline characteristics and long-term pain and complications were collected. Postoperative changes in PLP and PLS were recorded. Kaplan-Meier analysis was used to evaluate pain-free survival. Multivariate Cox regression analysis was performed to identify factors affecting pain outcomes. A total of 112 patients met the study inclusion criteria. With an average (range) follow-up of 47.4 (10-134) months, the long-term effectiveness and complication rate were 82.1% and 25.9%, respectively. Of 37 patients (33.0%) who developed PLS, 67.6% (25/37) experienced pain relief, whereas in 45.9% (17/37), PLS disappeared or changed after DREZ lesioning. Multivariate analysis showed that patients with shorter pain duration (≤5 years) and PLS had worse pain outcomes. This study revealed factors that predict the pain outcome of DREZ lesioning based on a large series of cases. The diverse postoperative changes in phantom limb indicate that the mechanisms underlying PLS and PLP at the spinal or supraspinal level may vary among patients with BPA. Future studies should investigate the contribution of maladaptive brain plasticity to the outcomes of patients undergoing DREZ lesioning.

Transcriptomic Profiling Reveals a Role for TREM-1 Activation in Enterovirus D68 Infection-Induced Proinflammatory Responses.

Increasing cases related to the pathogenicity of Enterovirus D68 (EV-D68) have made it a growing worldwide public health concern, especially due to increased severe respiratory illness and acute flaccid myelitis (AFM) in children. There are currently no vaccines or medicines to prevent or treat EV-D68 infections. Herein, we performed genome-wide transcriptional profiling of EV-D68-infected human rhabdomyosarcoma (RD) cells to investigate host-pathogen interplay. RNA sequencing and subsequent experiments revealed that EV-D68 infection induced a profound transcriptional dysregulation of host genes, causing significantly elevated inflammatory responses and altered antiviral immune responses. In particular, triggering receptor expressed on myeloid cells 1 (TREM-1) is involved in highly activated TREM-1 signaling processes, acting as an important mediator in EV-D68 infection, and it is related to upregulation of interleukin 8 (IL-8), IL-6, IL-12p70, IL-1ß, and tumor necrosis factor alpha (TNF-α). Further results demonstrated that NF-κB p65 was essential for EV-D68-induced TREM-1 upregulation. Moreover, inhibition of the TREM1 signaling pathway by the specific inhibitor LP17 dampened activation of the p38 mitogen-activated protein kinase (MAPK) signaling cascade, suggesting that TREM-1 mainly transmits activation signals to phosphorylate p38 MAPK. Interestingly, treatment with LP17 to inhibit TREM-1 inhibited viral replication and infection. These findings imply the pathogenic mechanisms of EV-D68 and provide critical insight into therapeutic intervention in enterovirus diseases.

Computer-Aided Rational Engineering of Signal Sensitivity of Quorum Sensing Protein LuxR in a Whole-Cell Biosensor.

LuxR, a bacterial quorum sensing-related transcription factor that responds to the signaling molecule 3-oxo-hexanoyl-homoserine lactone (3OC6-HSL). In this study, we employed molecular dynamics simulation and the Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) method to rationally identify residues in Vibrio fischeri LuxR that are important for its interaction with 3OC6-HSL. Isoleucine-46 was selected for engineering as the key residue for interaction with 3OC6-HSL-LuxR-I46F would have the strongest binding energy to 3OC6-HSL and LuxR-I46R the weakest binding energy. Stable wild-type (WT) LuxR, I46F and I46R variants were produced in Escherichia coli (E. coli) in the absence of 3OC6-HSL by fusion with maltose-binding protein (MBP). Dissociation constants for 3OC6-HSL from MBP-fusions of WT-, I46F- and I46R-LuxR determined by surface plasmon resonance confirmed the binding affinity. We designed and constructed a novel whole-cell biosensor on the basis of LuxR-I46F in E. coli host cells with a reporting module that expressed green fluorescent protein. The biosensor had high sensitivity in response to the signaling molecule 3OC6-HSL produced by the target bacterial pathogen Yersinia pestis. Our work demonstrates a practical, generalizable framework for the rational design and adjustment of LuxR-family proteins for use in bioengineering and bioelectronics applications.

De novo sequence redesign of a functional Ras-binding domain globally inverted the surface charge distribution and led to extreme thermostability.

To acquire extremely thermostable proteins of given functions is challenging for conventional protein engineering. Here we applied ABACUS, a statistical energy function we developed for de novo amino acid sequence design, to globally redesign a Ras-binding domain (RBD), and obtained an extremely thermostable RBD that unfolds reversibly at above 110°C, the redesigned RBD experimentally confirmed to have expected structure and Ras-binding interface. Directed evolution of the redesigned RBD improved its Ras-binding affinity to the native protein level without excessive loss of thermostability. The designed amino acid substitutions were mostly at the protein surface. For many substitutions, strong epistasis or significantly differentiated effects on thermostability in the native sequence context relative to the redesigned sequence context were observed, suggesting the globally redesigned sequence to be unreachable through combining beneficial mutations of the native sequence. Further analyses revealed that by replacing 38 of a total of 48 non-interfacial surface residues at once, ABACUS redesign was able to globally "invert" the protein's charge distribution pattern in an optimized way. Our study demonstrates that computational protein design provides powerful new tools to solve challenging protein engineering problems.

Clinical analysis of repeat microvascular decompression for recurrent hemifacial spasm.

The aim of this study was to investigate the effects of repeat microvascular decompression (MVD) for recurrent hemifacial spasm (HFS). The clinical features, surgical findings, outcomes, and complications of 13 patients who underwent MVD with a history of prior MVD in Xuanwu Hospital between January 2010 and May 2017 were analysed retrospectively. All patients were successfully treated for their HFS but experienced recurrent symptoms and received repeat MVD. Teflon felt factors (9/13, 69.2%) and vascular changes (4/13, 30.8%) were the main reasons for recurrent HFS. With a mean follow-up of 34.6 months after surgery (ranging from 12 to 92 months), 11 (84.6%) patients achieved complete or major spasm alleviation and two patients (15.4%) achieved fair outcomes. Surgical complications included transited mild to moderate facial weakness in two patients (15.4%). None of the patients had serious surgical morbidities. Repeat MVD is an effective and safe treatment for recurrent HFS.

Posterior percutaneous endoscopic cervical foraminotomy and discectomy for degenerative cervical radiculopathy using intraoperative O-arm imaging.

INTRODUCTION: Posterior percutaneous endoscopic cervical foraminotomy and discectomy (P-PECD) is a minimally invasive technique for the treatment of degenerative cervical radiculopathy. The O-arm, an intraoperative mobile computed tomography (CT) scanner, may improve spine surgery outcomes. AIM: To evaluate clinical outcomes of O-arm assisted P-PECD in patients with degenerative cervical radiculopathy. MATERIAL AND METHODS: Between January 2013 and January 2018, 32 patients with degenerative cervical radiculopathy who underwent P-PECD were followed up for 12 months. Their demographic, clinical and surgical data were reviewed retrospectively. All patients received intraoperative O-arm scanning to assess working cannula placement and decompression. The visual analogue scale (VAS), the neck disability index (NDI), and Odom's criteria were used to evaluate clinical outcomes. RESULTS: Compared with preoperative values, mean NDI, neck-VAS, and arm-VAS scores were dramatically improved 1 week postoperatively, and the improvement was maintained for at least a year after surgery (from 27.6 ±10.5, 5.8 ±1.7, and 7.2 ±2.3 to 1.4 ±0.8, 1.1 ±0.8 and 0.9 ±0.6, respectively). According to Odom's criteria, 27/32 patients (84.4%) reported excellent or good results. There were no permanent complications. One patient suffered from transient thumb weakness due to a cervical nerve root injury caused by the spinal needle. CONCLUSIONS: P-PECD aided by intraoperative O-arm imaging is a safe, effective, and minimally invasive procedure for treating degenerative cervical radiculopathy that can provide accurate cannula placement and thorough decompression.

Recurring sequence-structure motifs in (ßα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs.

An interesting way of generating novel artificial proteins is to combine sequence motifs from natural proteins, mimicking the evolutionary path suggested by natural proteins comprising recurring motifs. We analyzed the ßα and αß modules of TIM barrel proteins by structure alignment-based sequence clustering. A number of preferred motifs were identified. A chimeric TIM was designed by using recurring elements as mutually compatible interfaces. The foldability of the designed TIM protein was then significantly improved by six rounds of directed evolution. The melting temperature has been improved by more than 20°C. A variety of characteristics suggested that the resulting protein is well-folded. Our analysis provided a library of peptide motifs that is potentially useful for different protein engineering studies. The protein engineering strategy of using recurring motifs as interfaces to connect partial natural proteins may be applied to other protein folds.