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Aiming at the problem that traditional artificial fault diagnosis is inefficient and cannot meet the requirement of modern automobile intelligent development, a fault diagnosis technology for heavy truck ABS based on improved neural network is proposed in this paper. By analyzing the working principle of ABS system, this paper summarizes the common failure modes and causes of ABS. The data flow of ABS under different fault modes is collected through the real vehicle fault simulation test which is a scarce condition in current research. After pretreatment of the collected data, the BP neural network model optimized by LM algorithm is used to train the data. The model after training has high accuracy in predicting ABS-related faults, which is suitable for a wide range of applications, not only improving the efficiency and accuracy of ABS fault diagnosis, but also providing a new direction for the intellectualization of automobile fault diagnosis and maintenance.

Summary: Zika virus (ZIKV) infection causes Guillain-Barré syndrome and severe birth defects. ZIKV envelope (E) protein is the major viral protein involved in cell receptor binding and entry and is therefore considered one of the major determinants in ZIKV pathogenesis. Here we report a gene-wide mapping of functional residues of ZIKV E protein using a mutant library, with changes covering every nucleotide position. By comparing the replication fitness of every viral mutant between mosquito and human cells, we identified that mutations affecting glycosylation display the most divergence. By characterizing individual mutants, we show that ablation of glycosylation selectively benefits ZIKV infection of mosquito cells by enhancing cell entry, whereas it either has little impact on ZIKV infection on certain human cells or leads to decreased infection through the entry factor DC-SIGN. In conclusion, we define the roles of individual residues of ZIKV envelope protein, which contribute to ZIKV replication fitness in human and mosquito cells. : Entomology; Genomics; Virology; Protein Structure Aspects Subject Areas: Entomology, Genomics, Virology, Protein Structure Aspects

Avoiding interferon avoidance Interferon (IFN) expression is a mammal's first response to viral infection. Many viruses have thus evolved mechanisms to evade IFN. Du et al. developed a method to systematically ablate IFN evasion genes from live, attenuated influenza virus (see the Perspective by Teijaro and Burton). A combination of mutants was assembled to construct a virus that triggered transient IFN responses in mice but that was unable to replicate effectively. The transient IFN responses led to robust antibody and memory responses that protected against subsequent challenge with different influenza viruses. This approach could be adapted to improve other RNA virus vaccines. Science , this issue p. 290 ; see also p. 277

Background The accurate measurement of particulate matter (PM) provides a crucial basis for health impact assessment and pollution management and control. However, monitoring stations of air pollution are limited worldwide. Recently, some researchers have attempted to estimate the levels of PM based on remote sensing data, but the methods still need to be validated and further improved. Objectives This study aimed to develop a new model, to estimate daily ground-level PM2.5 concentrations using the fused aerosol optical depth (AOD) retrieved by the Moderate Resolution Imaging Spectro radiometer and meteorological information. Methods We combined generalized additive mixed-effects model with the log-linked Gaussian error distribution and non-linear exposure-lag-response model for AOD and meteorological measures, to estimate daily ground-level PM2.5 concentrations in 2014–2015 in Guangzhou, China. Results The PM2.5 concentration was significantly associated with AOD and meteorological measures. Compared to the log-linear model, the non-linear exposure-lag-response model had better model performance with a higher temporal (spatial) cross-validation R–square (0.81 (0.81) vs 0.67 (0.67)), and a smaller mean absolute percentage error (17.65% (16.90%) vs 21.22% (21.01%)). AOD explained about 15% variations of PM2.5 in the mixed-effect model. The planetary-boundary -layer-height-revised AOD and relative-humidity-revised PM2.5 did not significantly improve the model performance. Conclusion Considering the non-linear exposure-lag-response association between PM2.5 and AOD and meteorological factors can significantly increase the modelling ability to estimate PM2.5 concentrations.

The van der Waals forces between the layers of fluorphlogopite make it flexible, and its stability under strong acid, strong alkali, and high temperature conditions has potential applications as a new base material for flexible electronics. In this article, using magnetron sputtering technology, the focus is on the influence of the change of sputtering pressure on the photoelectric properties of the prepared ITO thin film. In this study, indium tin oxide (ITO) film samples were prepared on a fluorphlogopite substrate using the magnetron sputtering technique and adjusting the sputtering pressure from 0.6 Pa to 11 Pa at room temperature. The film was characterized using SEM, XRD, four-probe tester, and ultraviolet–visible spectrophotometer to understand its microstructure and photoelectric properties. The number of bending times of the sample's square resistance around the steel cylinder characterized its flexibility. The results showed that the sample crystal grains decreased significantly with the increase in pressure. Further, it can be seen from SEM images that all samples contained extremely uniform particles. The light transmittance and resistivity of the sample synthesized below 3 Pa increased sharply with the increase of sputtering pressure, and the change above 3 Pa tended to be stable. The average transmittance of visible light in the wavelength range of 400–800 nm ​​is higher than 86%, the highest being 92.7%; the sputtering pressure of 0.6 Pa yielded a sample with the lowest resistivity of 1.51 × 10−3 Ωcm. All the samples were bent 1200 times around a steel cylinder with a radius of 3.65 mm, and the change in sheet resistance did not exceed 5%.

Despite full immunoprophylaxis, mother-to-child transmission (MTCT) of Hepatitis B Virus still occurs in approximately 2–5% of HBsAg positive mothers. Little is known about the bottleneck of HBV transmission and the evolution of viral quasispecies in the context of MTCT. Here we adopted a newly developed tag linkage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immunoprophylaxis. By assigning unique tags to individual viral sequences, we accurately reconstructed HBV haplotypes in a region of 836 bp, which contains the major immune epitopes and drug resistance mutations. The detection limit of minor viral haplotypes reached 0.1% for individual patient sample. Dominance of “a determinant” polymorphisms were observed in two children, which pre-existed as minor quasispecies in maternal samples. In all four pairs of MTCT samples, we consistently observed a significant overlap of viral haplotypes shared between mother and child. We also demonstrate that the data can be potentially useful to estimate the bottleneck effect during HBV MTCT, which provides information to optimize treatment for reducing the frequency of MTCT.

Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance., Author summary Antiretroviral drugs have achieved great success in controlling the HIV pandemic. However, the therapy fails sometimes owing to the low drug adherence and/or the emergence of resistance associated mutations on viral genome. The persistence of drug resistance poses challenges in using antiretroviral drugs for long term control or pre-exposure prophylaxis. To understand the mechanisms of resistance evolution and persistence, we profiled the replication fitness of over 1000 HIV-1 mutants with combinations of resistance associated mutations on its protease gene. We found that although resistance associated mutations greatly reduce replication fitness, they interact positively to alleviate the mutational load. These genetic interactions, termed epistasis, increase the ruggedness along the evolution paths, restricting resistance associated mutations from reversal. Our data support the clinical observations that drug resistance mutations tend to persist even when antiretroviral drug is discontinued.

Dolutegravir (DTG) is a preferred drug for initial treatment of human immunodeficiency virus type 1 infection. We present next-generation sequencing analysis of integrase genotypes during a period of virologic failure in a treatment-naive man who initiated tenofovir disoproxil fumarate/emtricitabine plus DTG.

A finger severed with two or more planes on its vertical axis is called a multi-section severing or multi-plane severing. Replantation of a multi-section severed finger is one of the most serious types. There is more than one anastomotic stoma in the same finger and if an embolism occurred in any one of them, partial necrosis or total necrosis is inevitable, and the risk of a vascular crisis is greatly increased. It is by no means a simple accumulation of single-section replantation, it is uncommon clinically, and it is caused by cutting machines and punch failure. The different position of hand, the shape of the cutting tool, and the speed of the machine will cause different injuries. Multi-section replantation develops based on single-section replantation and it is of the difficulty of hand surgery because of the serious injury, complex conditions, multiple surgical sites, greater difficulty, higher technical requirements, and longer operation time. In most cases, such patients will accept stump revision, which greatly affects the appearance and function. However, in the highly developed microsurgery of today, if the severed tissue is relatively complete, replantation should be considered.

Amputated fingers are not uncommon today because of mechanical accidents, traffic accidents, and other hazards. Replantation is the best method of recovery for amputated fingers. At present, the survival rate of replantation-receiving patients is more than 90%, no matter whether they have an amputation of one finger or all ten fingers, and the postoperative appearance and function are good. To achieve successful replantation does not just depend on the simple replantation and postoperative treatment, and preoperative preparation is also a prerequisite; thus, surgeons should spare enough time to carry out proper preoperative preparations. Routine preoperative preparation includes: (a) Drying and refrigeration are the main methods of storage for amputated fingers, which cannot be soaked in water or disinfectant and can be placed among ice blocks in summer. (b) The wound should be pressurized and bandaged with clean gauze in the case of emergency treatment. (c) Psychological preparation is needed for postoperative recovery. (d) General assessments should be performed by a doctor before the operation to rule out life-threatening risks, determine the indications, and rule out any contraindications. (e) Preoperative preparations for surgical fields and surgical instruments and materials.

Replantation of amputated finger is a detailed and difficult project, requiring surgeons to perform the operation all through the course under the surgical microscope. Besides basic knowledge of orthopedics, vascular surgery, plastic surgery, it is necessary to being proficient in microsurgery technology operation, to achieve stable, accurate, skillful operating skills. According to the general principles, the order of replantation and the specific circumstances, flexible control and temporary adjustment of the surgical plan is needed to ensure that every step of the operation is correct. There are two orders of replantation of amputated fingers. One is antegrade replantation, using by most scholars conventionally, that debridement—skeletal fixation—repair of the flexor and extensor tendon—dorsal vein anastomosis-dorsal skin suture—inherent artery anastomosis—nerve anastomosis-palmar skin suture. The other one is retrograde replantation: debridement-palmar skin suture—finger nerve anastomosis—inherent arteries anastomosis—flexor tendon suture- skeletal fixation—extensor tendon suture—dorsal vein anastomosis-dorsal skin suture. The latter has the advantage of not having to turn over the hands during the surgical procedure, especially for replantation of thumb amputation, and severed fingers in children. Avoiding to pull and sprain the anastomosed blood vessels and nerves when a fracture is fixed. The specific operation are as follows (Fig. 7.1).

Replantation of an amputated finger refers to a surgery on the complete or incomplete amputated finger(s) during which the vessels, nerves, tendons, bones, and skin are re-anastomosed and repaired to make the amputated fingers recover certain functions. It is characterized by a complex surgical process, accurate operation, long duration, and the need for complete immobilization. The requirements for anesthesia are a simple operation, a small impact on the patient’s physiological functions, complete immobilization, painlessness during the operation, easy monitoring, perfect postoperative analgesia, maintenance of dilation of local small vessels, and reduction of vasospasm. This chapter focuses on the common anesthesia modes for replantation of amputated fingers.

Rotation avulsion of fingers is usually caused by a fast rotating machine with a roller and occurs in the left thumb. In most patients, it is characterized by the following: (a) The skin is stripped with the subcutaneous tissue, which is like a flap or avulsion injury. (b) The extensor and flexor tendons are usually pulled out. (c) The digital veins are usually broken near the edge of the skin. (d) The digital nerves are usually pulled out with uneven ends because they are relatively strong. (e) The toughness of the arteries is stronger than that of the veins, but they are weaker than the nerves; thus, they are broken earlier than nerves and later than veins, which is easily understood.

Rehabilitation refers to the comprehensive coordination and application of medical, educational, occupational, social, and other methods, making it possible for sick, injured, and disabled persons (including those with congenital disability) who have lost function to restore and reconstruct to the maximum extent as soon as possible, allowing them to recover their ability in physical, mental, social, and financial states as much as possible, bringing them back to life, back to work, back to society (WHO). Rehabilitation is not only for the disease, but also for the whole person, from physical, psychological, social, and financial abilities to comprehensive rehabilitation.

A self-mutilated severed finger is when the patient cuts his own finger off if he or she has an emotional disorder, depression or is intoxicated. It is characterized by the following: (a) Most cases are young men with a bad temper. (b) Most fingers severed in this way comprise the middle and final segments of the left little finger. (c) The wound is smooth with no other injuries, which makes it easy to replant. (d) The patient does not cooperate with treatment for a long time as he or she has so many negative emotions such as regret, angry, and guilt. (e) The replantation is easier compared with other replantations, but postoperative nursing is more difficult because of the patients’ noncompliance.

The replantation of severed fingers of old people relates to those whose over 60 years old. With the development of basic and clinical research, age is no longer a contraindication. If old people suffer severed fingers, their general condition should be assessed first to judge whether they can tolerate surgery, and then consideration should be given to whether or not they wish to undergo replantation and to ensure they understand the function of replanted finger. Any operative treatment should be considered on the assumption of a relatively good condition of the severed finger, short ischemia, good general condition, controlled internal diseases and expected good function recovery. The replantation of severed fingers of old people is always a challenge in clinical practice because of its specificity, but the age range of successful replantation is growing. There was successful case reported for a 72-year-old at No 153 Central Hospital of the People’s Liberation Army in 1990, and for a 74-year-old at No 89 Hospital of the People’ Liberation Army. Another successful case, for a 79-year-old, was described in Hand Surgery, edited by Gu Yudong, Wang Shuhuan and Shi De in 2000.

Severed tissues should be replanted within 6 h at room temperature (20–25 °C), as irreversible necrosis of the muscles occurs because of ischemia. The time can be increased to 12 h if refrigerated (4 °C). The ischemia time for fingers without muscles could be 8 h at room temperature and 12 h under refrigeration. The replantation of a finger whose warm ischemia time is over the time limit is called late replantation. There are very few successful reports of late replantation, and most of these are case reports.

China’s amputated finger replantation technology is in the leading position worldwide in terms of replantation techniques, the number of cases, replantation difficulty, and survival rate after development for nearly 50 years. The success of the replantation of an amputated finger is related to multiple factors such as the patient’s injuries, vascular conditions, and quality of intraoperative vascular anastomosis, and is also closely associated with the postoperative treatment and management. If there is no emphasis on post-replantation treatment and management, the surgery will fail. Special attention should be paid to the vascular crisis (spasm and embolism) that occurs after the replantation of an amputated finger. Treatment and management are of great importance after the replantation of an amputated finger to improve the success rate of replantation.

Hand surface landmarks include skin landmarks, bony landmarks, and tendon (muscle) landmarks. These landmarks are exposed to varying extents when the hand has different statuses. Therefore, they can appear more apparent when moving different joints during clinical applications.

Finger replantation is an important part of microsurgery, and the key to success is fine blood vessels and nerve anastomosis. Finger blood vessels and nerves are very small; thus, it is very difficult to distinguish them with the naked eye. All surgical protocols must be performed with a microscope, micro-instruments and various special repair materials. The development of the replantation of amputated fingers is closely connected to the development of surgical equipment and materials. It is the continuous development of surgical equipment and materials that promotes the development of replantation of amputated fingers. Below, some of the commonly used equipment and materials for finger replantation are described (Fig. 3.1).

With amputated tissue mass of fingers, some parts’ continuity with the finger body is broken, including bones, joints, tendons, vessels, and nerves, which cannot survive without vascular anastomosis. It is different from general replantation of severed fingers in these respects: (a) The tissues are usually separate from each other. (b) No well-known vessels or nerves to be matched or just pass away. (c) They are difficult to replant and microsurgical techniques are required because the anatomy of the amputated tissues is not clear, but the appearance and functioning will be good if the surgery succeeds.

With the development of industry and agriculture, and diversification of the automatic machine, there are and increasing number of types of severed fingers including those with soft-tissue defects. Soft-tissue defects include defect of the skin, vessels, and nerves, and there is a lack of a regular method for repair because of the complicated conditions, the variety of injuries, and variety of ways to repair them. Professional microsurgical techniques and a knowledge of flaps are required for surgeons so that they choose a suitable flap for repair according to the type of injury and the extent, position, and scope of the defect. Soft-tissue defect was listed as a contraindication for replantation in the 1980s. The replantation used to be applied by shortening bones that would survive, but without satisfactory appearance and function. Sometimes, to preserve the joints and length of the fingers, palliative debridement may cause infection, necrosis of the skin, and poor blood supply, which will affect finger survival or the finger survives, but the functioning is affected by the shortened finger, poor sensation, severe tendon adhesion, and stiff joints. With the development of microsurgery techniques and the maturity of flaps, vessels, tendons, flaps, and composite tissue flaps can be used to repair the soft-tissue defects of severed fingers to reduce postoperative vascular crisis, increase the survival rate, and expand the indications for replantation.

The successful replantation of amputated fingers is based on not only the microsurgery technique, but also the medicines used postoperatively. Three kinds of medicines are generally used after an operation, which are antibiotics, antispasmodics, and anticoagulant drugs. Antibiotics must be used intraoperatively and postoperatively because of complex injuries, the long duration, and prolonged exposure of the wound. The common reasons why the antispasmodic drugs and anticoagulant drugs should be used after an operation are: 1. Blood coagulability is increased after injury and operation, which is the body’s protective physiological response 2. Adrenaline is released after the injury and operation; thus, patients are prone to experiencing vasospasm, an increase in platelets and an increase in blood coagulation, which easily leads to thrombosis 3. Spasticity and thrombosis can be easily induced because of the small diameter, which is commonly 1–3 mm (a minimum of 0.2–0.5 mm), and easy susceptibility to physicochemical factors 4. There is a higher chance of thrombosis because of the small scouring force to anastomotic stoma caused by the small diameter and low blood flow. It is necessary to use antispasmodic drugs and anticoagulant drugs because experiments have proved that the smaller diameter of the vessel, the more likely it is that thrombosis will occur, because the 1-mm vessel has a platelet absorption density twice as high as the 2-mm vessel. In Table 4.1, the commonly used drugs are shown.

The hand is an organ related to labor and beauty that distinguishes humans from other animals. As human civilization progresses, the hands play an irreplaceable role in the process when human activities shift from handicraft to light industry, heavy industry, and electronic technology information. Hands are most susceptible to damage during daily life and work. During industrial production in particular, with relatively low automaticity, it is not uncommon for severe traumas caused by high energy in the hands to result in finger mutilation, leading to life-long disability. Surgeons face the arduous task of attempting to repair and reconstruct the injuries, reduce the patient’s disability and improve their quality of life. Human efforts to carry out studies of hand trauma have never ceased, whether the study be fundamental or clinical. The simple trauma care of hand injuries has been directed to evolve toward the complicated replantation of mutilated fingers and the recovery of hand functions. Long-term clinical practice has demonstrated that patient cooperation and reasonable functional exercise is also of vital significance during the treatment of hand trauma, in addition to the doctor’s accurate judgment, skill proficiency, and proper management. Satisfying results can be achieved in the recovery of hand trauma only after the joint efforts of both doctors and patients.

The final segment of the finger is the furthest structure of the hand, the most frequently used in daily life, and has the highest rate of injury; thus, replantation of the final segment of the finger (fingertip) is common. The functioning of the finger will be seriously affected if the final segment is missing, even though it is small. Compared with the flap method of retaining the length of the finger, replantation is irreplaceable in the recovery of appearance, movement, and feeling. In principle, if the systemic condition of the patients permitted it, if the structure of the severed finger was more or less complete, and if patients and their families required replantation, replantation should be chosen whenever possible.

Severed finger with avulsion is also called a ring avulsed finger that is combined with avulsed arteries and nerves, which are difficult to repair. It usually occurs in workers wearing gloves to operate a high-speed spinning machine or a finger with a ring whose entire soft tissue was avulsed like taking off the gloves, including skin, subcutaneous tissue, vessels, and nerves, just leaving the bones, joints, and tendons. It is characterized by: (a) The destroyed finger has a blunt injury, which is much heavier than the distal part. (b) The avulsed tissues are not in the same plane or even the same tissue. (c) The avulsed vessels and nerves are usually long and may not be able to be used. (d) The finger body of the destroyed finger is usually contused to different degrees.

If the severed part is complete, but the proximal part is seriously damaged or the general condition of the patient does not permit surgery, the severed part could be implanted to another position before being implanted to the in-situ position to recover the appearance and function. This therapy method is called ectopic implantation.

The left hand of a 38-year-old female was injured by an injection molding machine and she was admitted within an hour. Physical examination: The general situation was good, and the vital signs were stable. We found only the thumb and the proximal–distal parts of the ring and little fingers were still residual. The wound was bleeding, irregular with multiple fractures, with tendon, blood vessel, and broken nerve ends exposure. There was no blood supply for the residual fingers, so they were shifted and replanted to metacarpal and radial alignment after satisfactory debridement under anesthesia and fixed with 1.0-mm Kirschner wire. After that, the tendons, blood vessels, and nerves were also anastomosed one by one. The surgery was successful since the replanted fingers were ruddy, with moderate tension and after the tourniquet relaxed. The patient was brought to the ward safely after the operation with the replanted finger fixed with a sterile cotton bandage and padded with broken cotton yarn. Then, the conventional treatment was given to her, and the replanted severed finger successfully survived 2 weeks later. The replanted finger’s function and growth are good after regular follow-up and functional exercise guidance. (Fig. 8.1).

Multiple severed fingers means two or more fingers severed, what is more complicated than would occur in one hand or both hands. Most cases are caused by mechanical damage and the rest are caused by knife cuts or other penetrating trauma. Multiple severed fingers are a common hand injury, compared with a single severed finger, it is characterized by: (a) More serious trauma, a more complicated condition, more blood loss, which would cause changes in blood volume, blood components, and hemodynamics, and activate systemic compensatory vasoconstriction. (b) Longer operating time, more difficulty, which requires not only more energy and stamina from the surgeon, but also a stricter anesthesia way and perioperative period treatment. (c) Higher microtechnical requirements of racing against time to reduce the ischemia time of severed fingers. (d) Close observation of the replanted fingers after the operation and maintaining general stability to prevent high coagulation, while preventing excessive bleeding.

Zika virus (ZIKV) infection causes Guillain-Barré syndrome and severe birth defects. ZIKV envelope (E) protein is the major viral protein involved in cell receptor binding and entry and therefore considered one of the major determinants in ZIKV pathogenesis. Here, we report a gene-wide mapping of functional residues of ZIKV E protein using a mutant library with changes covering every nucleotide position. By comparing the replication fitness of every viral mutant between mosquito and human cells, we identified that mutations affecting N-linked glycosylation at N154 position display the most divergence. Through characterizing individual mutants, we show that, while ablation of N-linked glycosylation selectively benefits ZIKV infection of mosquito cells by enhancing cell entry, it either had little impact on ZIKV infection on certain human cells or decreased infection through entry factor DC-SIGN. In conclusion, we define the roles of individual residues of ZIKV envelope protein, which contribute to ZIKV replication fitness in human and mosquito cells.HighlightsGene-wide mapping of functional residues of E protein in human and mosquito cells.Mutations affecting N-linked glycosylation display the most dramatic difference.N-linked glycosylation decreases ZIKV entry into mosquito cells.N-linked glycosylation is important for DC-SIGN mediated infection of human cells.

Certain Major Histocompatibility-I (MHC-I) types are associated with superior immune containment of HIV-1 infection by CD8+ cytotoxic T lymphocytes (CTLs), but the mechanisms mediating this containment are difficult to elucidate in vivo. Here we provide controlled assessments of fitness landscapes and CTL-imposed constraints for immunodominant epitopes presented by two protective (B*57 and B*27) and one non-protective (A*02) MHC-I types. Libraries of HIV-1 with saturation mutagenesis of CTL epitopes are propagated with and without CTL selective pressure to define the fitness landscapes for epitope mutation and escape from CTLs via deep sequencing. Immunodominant B*57- and B*27- present epitopes are highly limited in options for fit mutations, with most viable variants recognizable by CTLs, whereas an immunodominant A*02 epitope-presented is highly permissive for mutation, with many options for CTL evasion without loss of viability. Generally, options for evasion overlap considerably between CTL clones despite highly distinct T cell receptors. Finally, patterns of variant recognition suggest population-wide CTL selection for the A*02-presented epitope. Overall, these findings indicate that these protective MHC-I types yield CTL targeting of highly constrained epitopes, and underscore the importance of blocking public escape pathways for CTL-based interventions against HIV-1., Author summary Certain MHC class I types are associated with superior immune containment of HIV-1, underscoring the importance of CD8+ cytotoxic T lymphocytes (CTLs). Epitope escape mutations for these types is limited, indicating reduced immune evasion. Two proposed mechanisms are: 1) CTL targeting of highly sequence-constrained epitopes, or 2) more promiscuous CTLs for epitope variation. However, the in vivo complexity of undefined starting virus, multiple targeted epitopes, polyclonal CTL responses against each epitope, and post-hoc evaluation of the interaction renders examination of mechanisms difficult. Here we approach this question with controlled prospective in vitro experiments using saturation mutagenesis of epitopes in clonal HIV-1, propagated in the absence or presence of CTL clones to define the options for epitope mutation and immune evasion by deep sequencing. We find that two immunodominant epitopes presented by protective MHC types are highly mutation-constrained compared to one presented by a non-protective MHC type, whereas CTL promiscuity for epitope variation is not appreciably different. These results suggest that these protective MHC types are associated with limited HIV-1 escape predominately due to intrinsic constraints on epitope mutation, and underscore the importance of focusing the CTL response on highly conserved epitopes for immunotherapies and vaccines.

In recent years, modified liquid crystal (LC) material has been widely applied in display industry for outstanding performances by changing the prescription or adding additives. Polymer stabilised cholesteric liquid crystal (PSCLC) was designed with the aim for achieving better performance. In this study, a stable system was established by doping FexNiy nanoparticles into a PSCLC film, in which nanoparticles (NPs) were modified by organic LC molecules. The NPs composite were monodispersed evenly in PSCLC film without agglomeration. The electrical-optical performance was improved in different ways. The minimum reported response time of FeNi, FeNi3 and Ni was 3.32, 3.45 and 4.32 ms, which showed 72.33%, 71.25% and 64% reduction, respectively. However, the drive voltage of FeNi, FeNi3 and Ni was 6.92, 6.58 and 6.84 V which showed 61.56%, 63.44% and 62% reduction, respectively. The viewing angle of PSCLC was extended. Besides, as the drive frequency was raised by 5 kHz, Vth dropped from 6.58 to 1.62 V, and de...

Cholesteric liquid crystal (CLC) with helically aligned molecules, demonstrates unique optical features. Conventionally, such structure reflects a maximum 50% of unpolarised light. Polymer-stabilised CLC was designed to exceed the limit by mixing liquid crystal (LC) and a photopolymerisable monomer of opposite chirality. The reflectance was carefully investigated and the result was 55.7% in the visible region at room temperature, where it exceeded the theoretical limit. Such phenomena were studied and theoretical model was discussed. Electro-optical test showed the driving voltage was of LC cell was slightly changed after polymerisation.

Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available., IMPORTANCE To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available.

Background The high error rate of next generation sequencing (NGS) restricts some of its applications, such as monitoring virus mutations and detecting rare mutations in tumors. There are two commonly employed sequencing library preparation strategies to improve sequencing accuracy by correcting sequencing errors: read-pairing method and tag-clustering method (i.e. primer ID or UID). Here, we constructed a homogeneous library from a single clone, and compared the variant calling accuracy of these error-correction methods. Result We comprehensively described the strengths and pitfalls of these methods. We found that both read-pairing and tag-clustering methods significantly decreased sequencing error rate. While the read-pairing method was more effective than the tag-clustering method at correcting insertion and deletion errors, it was not as effective as the tag-clustering method at correcting substitution errors. In addition, we observed that when the read quality was poor, the tag-clustering method led to huge coverage loss. We also tested the effect of applying quality score filtering to the error-correction methods and demonstrated that quality score filtering was able to impose a minor, yet statistically significant improvement to the error-correction methods tested in this study. Conclusion Our study provides a benchmark for researchers to select suitable error-correction methods based on the goal of the experiment by balancing the trade-off between sequencing cost (i.e. sequencing coverage requirement) and detection sensitivity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2388-9) contains supplementary material, which is available to authorized users.

Background Epistasis is one of the central themes in viral evolution due to its importance in drug resistance, immune escape, and interspecies transmission. However, there is a lack of experimental approach to systematically probe for epistatic residues. Results By utilizing the information from natural occurring sequences and high-throughput genetics, this study established a novel strategy to identify epistatic residues. The rationale is that a substitution that is deleterious in one strain may be prevalent in nature due to the presence of a naturally occurring compensatory substitution. Here, high-throughput genetics was applied to influenza A virus M segment to systematically identify deleterious substitutions. Comparison with natural sequence variation showed that a deleterious substitution M1 Q214H was prevalent in circulating strains. A coevolution analysis was then performed and indicated that M1 residues 121, 207, 209, and 214 naturally coevolved as a group. Subsequently, we experimentally validated that M1 A209T was a compensatory substitution for M1 Q214H. Conclusions This work provided a proof-of-concept to identify epistatic residues by coupling high-throughput genetics with phylogenetic information. In particular, we were able to identify an epistatic interaction between M1 substitutions A209T and Q214H. This analytic strategy can potentially be adapted to study any protein of interest, provided that the information on natural sequence variants is available. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2358-7) contains supplementary material, which is available to authorized users.

Melatonin (C₁₃H₁₆N₂O₂) has a wide range of functions in the body. When is inappropriately exposed to light at night, human circadian rhythm will be interfered and then melatonin secretion will become abnormal. For nearly three decades great progresses have been achieved in analytic action spectra and melatonin suppression by various light conditions. However, so far few articles focused on the quantitative calculation of melatonin suppression induced by light. In this article, an algorithm is established, in which all the contributions of rods, cones, and intrinsically photosensitive retinal ganglion cells are considered. Calculation results accords with the experimental data in references very well, which indicate the validity of this algorithm. This algorithm can also interpret the rule of melatonin suppression varying with light correlated color temperature very well.

As an important hormone, melatonin has a wide range of functions in human body. Inappropriate light at night (LAN) will cause abnormal human circadian rhythm and then lead to melatonin secretion suppression. Melatonin suppression depends on correlated color temperature (CCT) and wavelengths of LAN. So far there was no quantitative algorithm for melatonin suppression by LAN. A relative spectral sensitivity curve of human plasma melatonin suppression was fitted and an algorithm was presented for predicting melatonin suppression by LAN. Theoretical basis and a method were provided for instructing safety strategy of architectural light at night. Also, the results could be applied in controlling light pollution, formulating the standard of safety nocturnal environment illumination and some other fields.

Luminescent cholesteric liquid crystalline polymers consisting of the lanthanide ions covalently attached to cholesteric polysiloxanes are prepared. Cholesteric liquid crystalline monomer and 4-(allyloxy)benzoic acid grafted to poly(methylhydrogeno)siloxane is used as one of the precursors for the preparation of the lanthanide-containing cholesteric liquid crystalline polymers. The chemical structures of the monomers are characterised by Fourier transform infrared, 1H NMR and elemental analyses. The mesomorphic properties and phase behaviour are investigated by differential scanning calorimetry, thermogravimetric analysis, polarising optical microscopy and X-ray diffraction. The polymers containing

A fiber probe-based positioning scan approach was established, whose precision can reach as high as 0.8 μm. And a set of modified microscope system was designed utilizing this approach, in which the scanning probe microscope (SPM) combined with an optical microscope was manipulated. The optical microscope and scanning probe can conveniently be switched through a switch panel. The observation period of samples can significantly be shortened. And more reliable images can be provided using this approach. Our design can effectively solve the inherent disadvantages of SPM technology, which makes SPM scan and image more reliably, conveniently, safely and rapidly.

The local near-field light scattering and the series dynamic progress of dyestuff PAN particles in solution were investigated taking advantage of optical fiber probe and the near-field detection techniques, including the dissolving and crystallizing progress, Brownian movement and the statistical distribution of particles. Some useful and interesting results were obtained, and are in good agreement with the theoretical analysis. These findings will contribute to the research of near-field optics in a liquid environment as well as provide direct and valuable results for statistical physics.

Summary The fiber micro-probe for near-field scanning optical microscope (NSOM) was fabricated using end-fixed laser-assisted melting and pulling method. The scanning electron microscope (SEM) observation showed that the fiber probes obtained by this method possessed small diameter of tip and large conic angle. The reproducibility came close to 70%. The effects of various fabrication parameters on probes were investigated, including laser power, pulling force, and the diameter of melting zone. The optimal processing conditions were derived based on the experiments and theoretical analysis. This research provides an alternative and advantageous method for fabrication of high-quality fiber probes.