NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.

MOTIVATION: Structural variants (SVs) play a causal role in numerous diseases but can be difficult to detect and accurately genotype (determine zygosity) with short-read genome sequencing data (SRS). Improving SV genotyping accuracy in SRS data, particularly for the many SVs first detected with long-read sequencing, will improve our understanding of genetic variation. RESULTS: NPSV-deep is a deep learning-based approach for genotyping previously reported insertion and deletion SVs that recasts this task as an image similarity problem. NPSV-deep predicts the SV genotype based on the similarity between pileup images generated from the actual SRS data and matching SRS simulations. We show that NPSV-deep consistently matches or improves upon the state-of-the-art for SV genotyping accuracy across different SV call sets, samples and variant types, including a 25% reduction in genotyping errors for the Genome-in-a-Bottle (GIAB) high-confidence SVs. NPSV-deep is not limited to the SVs as described; it improves deletion genotyping concordance a further 1.5 percentage points for GIAB SVs (92%) by automatically correcting imprecise/incorrectly described SVs. AVAILABILITY AND IMPLEMENTATION: Python/C++ source code and pre-trained models freely available at https://github.com/mlinderm/npsv2.

Palladium-Catalyzed Carbonylation Reaction of Indole/Pyrrole Involving HCFO-1233zd (E).

3-Indole-3-one is a key intermediate in the synthesis of many drugs and plays an important role in synthetic chemistry and biochemistry. A new method for synthesizing trifluoromethylated 3-indoleketones by Pd(0)-catalyzed carbonylation was introduced. In the absence of additives, 1-chloro-3,3,3-trifluoropropyl (an inexpensive and environmentally friendly synthetic block of trifluoromethyl) reacts with indole and carbon monoxide to generate trifluoromethylindole ketones with good yields, regioselectivity, and chemical selectivity; furthermore, the products exhibit strong resistance to basic functional groups, such as alkynes, aldehydes, and esters. In addition to the conversion of indole compounds into corresponding products, pyrrole and heteroindole may be suitable for corresponding chemical transformations. This study provides a synthetic method for the further construction of trifluoromethylated 3-indole ketones.

The effects of emotion on retrospective duration memory using virtual reality.

Our memories for temporal duration may be colored by the emotions we experience during an event. While emotion generally enhances some aspects of memory, temporal duration has been shown to be particularly susceptible to emotion-induced distortions. However, prior work has faced difficulty when studying this phenomenon, having to make some trade-offs on ecological validity or experimental control. Here, we sought to bridge this gap by studying the effects of emotion on temporal duration memory using virtual reality. In the present study, a final sample of 69 participants experienced a series of negative-emotional and neutral worlds within virtual reality. Following this, participants provided ratings of emotionality (arousal, valence, pleasantness) and retrospective duration estimates (i.e., remembered time). We hypothesized that negative events would be recalled as having a greater duration than neutral events (H1). We additionally hypothesized that negative, but not neutral, events would be recalled as being longer than the true duration (H2). The results supported H1 while failing to provide evidence in support of H2. Together, the results bolster the importance of emotion, especially negative emotion, in shaping how we remember the temporal unfolding of the past.

Application of Metal-Based Catalysts for Semi-Hydrogenation of Alkynol: A Review.

Alkynol semi-hydrogenation plays a vital role in industrial processes, due to the significance of its main product, enol, in high-end chemical synthesis, such as medicine, pesticide, food additives, and polymer monomer synthesis. Multiple intermediates are formed through a complex series of parallel or continuous reactions under varying conditions. However, the selectivity and efficiency of catalysts for producing these products still pose significant challenges. This review aims to thoroughly discuss the challenges and advancements in catalysts using different species and supports under various reaction conditions. Furthermore, strategies to enhance the yield and rate of enols are summarized based on noble metals, non-noble metals, and metal comparisons. By addressing diverse catalysts and reaction conditions, this review provides valuable insights into improving the semi-hydrogenation of acetylenic alcohols to enols.

Cooperative Effect of Ni-Decorated Monolayer WS2, NiO, and AC on Improving the Flame Retardancy and Mechanical Property of Polypropylene Blends.

Improving the residual char of polypropylene (PP) is difficult due to the preferential complete combustion. Here, we designed a combination catalyst that not only provides physical barrier effects, but also dramatically promotes catalytic charring activity. We successfully synthesized WS2 monolayer sheets decorated with isolated Ni atoms that bond covalently to sulfur vacancies on the basal planes via thiourea. Subsequently, PP blends composed of 8 wt.% Ni-decorated WS2, NiO, and activated carbon (AC) were obtained (ENi-SWS2-AC-PP). Combining the physical barrier effects of WS2 monolayer sheets with the excellent catalytic carbonization ability of the ENi-SWS2-AC combination catalyst, the PP blends showed a remarkable improvement in flame retardancy, with the yield of residual char reaching as high as 41.6 wt.%. According to scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations, it was revealed that the microstructure of residual char contained a large number of carbon nanotubes. The production of a large amount of residual char not only reduced the release of pyrolytic products, but also formed a thermal shield preventing oxygen and heat transport. Compared to pure PP, the peak heat release rate (pHRR) and total heat release rate (THR) of ENi-SWS2-AC-PP were reduced by 46.32% and 26.03%, respectively. Furthermore, benefiting from the highly dispersed WS2, the tensile strength and Young's modulus of ENi-SWS2-AC-PP showed similar values to pure PP, without sacrificing the toughness.

Ion-Dipole Interaction Enabling Highly Efficient CsPbI3 Perovskite Indoor Photovoltaics.

Metal halide perovskites are ideal candidates for indoor photovoltaics (IPVs) because of their easy-to-adjust bandgaps, which can be designed to cover the spectrum of any artificial light source. However, the serious non-radiative carrier recombination under low light illumination restrains the application of perovskite-based IPVs (PIPVs). Herein, polar molecules of amino naphthalene sulfonates are employed to functionalize the TiO2 substrate, anchoring the CsPbI3 perovskite crystal grains with a strong ion-dipole interaction between the molecule-level polar interlayer and the ionic perovskite film. The resulting high-quality CsPbI3 films with the merit of defect-immunity and large shunt resistance under low light conditions enable the corresponding PIPVs with an indoor power conversion efficiency of up to 41.2% (Pin : 334.11 µW cm-2 , Pout : 137.66 µW cm-2 ) under illumination from a commonly used indoor light-emitting diode light source (2956 K, 1062 lux). Furthermore, the device also achieves efficiencies of 29.45% (Pout : 9.80 µW cm-2 ) and 32.54% (Pout : 54.34 µW cm-2 ) at 106 (Pin : 33.84 µW cm-2 ) and 522 lux (Pin : 168.21 µW cm-2 ), respectively.

Research on Wide-Temperature Rechargeable Sodium-Sulfur Batteries: Features, Challenges and Solutions.

Sodium-sulfur (Na-S) batteries hold great promise for cutting-edge fields due to their high specific capacity, high energy density and high efficiency of charge and discharge. However, Na-S batteries operating at different temperatures possess a particular reaction mechanism; scrutinizing the optimized working conditions toward enhanced intrinsic activity is highly desirable while facing daunting challenges. This review will conduct a dialectical comparative analysis of Na-S batteries. Due to its performance, there are challenges in the aspects of expenditure, potential safety hazards, environmental issues, service life and shuttle effect; thus, we seek solutions in the electrolyte system, catalysts, anode and cathode materials at intermediate and low temperatures (T < 300 °C) as well as high temperatures (300 °C < T < 350 °C). Nevertheless, we also analyze the latest research progress of these two situations in connection with the concept of sustainable development. Finally, the development prospects of this field are summarized and discussed to look forward to the future of Na-S batteries.

Synergistic Effect of Activated Carbon, NiO and Al2O3 on Improving the Thermal Stability and Flame Retardancy of Polypropylene Composites.

It is difficult to enhance the char yields of polypropylene (PP) due to the preferential complete combustion. Successful formation of abundant char layer structure of PP upon flammability was obtained due to the synergistic effect of NiO, Al2O3 and activated carbon (AC). From characterization of scanning electron microscopy (SEM) and transmission electron microscopy (TEM), it was revealed that the microstructure of residual char contained large amount of carbon nanotubes. Compared to the modification of AC, NiO and Al2O3 alone, the combination of AC, NiO and Al2O3 dramatically promotes the charring ability of PP. In the case of AC and NiO, NiO plays a role of dehydrogenation, resulting in the degradation product, while AC mainly acts as carbonization promoter. The addition of Al2O3 results in higher dispersion and smaller particle size of NiO, leading to greater exposure of active sites of NiO and higher dehydrogenation and carbonization activity. Compared to the neat PP, the decomposition temperature of the PP modified by combined AC, NiO and Al2O3 was increased by 90 ℃. The yield of residual char of AC-5Ni-Al-PP reached as high as 44.6%. From the cone calorimeter test, the heat release rate per unit area (HRR) and total heat release per unit area (THR) of PP composite follows the order AC-5Ni-Al-PP < AC-10Ni-Al-PP < AC-Ni-PP < AC-15Ni-Al-PP < AC-1Ni-Al-PP. Compared to the neat PP, the peak of HRR declined by 73.8%, 72.7%, 71.3%, 67.6% and 62.5%, respectively.

Low-Dimensional Phase Regulation to Restrain Non-Radiative Recombination for Sky-Blue Perovskite LEDs with EQE Exceeding 15 .

Achieving efficient blue electroluminescence (EL) remains the fundamental challenge that impedes perovskite light-emitting diodes (PeLEDs) towards commercial applications. The bottleneck accounting for the inefficient blue PeLEDs is broadly attributed to the poor-emissive blue perovskite emitters based on either mixed halide engineering or reduced-dimensional strategy. Herein, we report the high-performing sky-blue PeLEDs (490 nm) with the maximum EQE exceeding 15 % by incorporating a molecular modifier, namely 4,4'-Difluorophenone, for significantly suppressing the non-radiative recombination and tuning of the low-dimensional phase distribution of quasi-2D blue perovskites, which represents a remarkable paradigm for developing the new generation of blue lighting sources.

Light-Triggered Sustainable Defect-Passivation for Stable Perovskite Photovoltaics.

The generation of photoinduced defects and freely moving halogen ions is dynamically updated in real time. Accordingly, most reported strategies are static and short-term, which make their improvements in photostability very limited. Therefore, seeking new passivation strategies to match the dynamic characteristics of defect generation is very urgent. Without newly generated defects, a passivation molecule should exist in the configuration that would not become the initiation sites for defect generation. With newly generated defects, the passivation molecule should transfer into the other configuration that possesses the passivation sites. Herein, a classical photoisomeric molecule, spiropyran, is adopted, whose pre- and post-isomeric forms meet the requirements for two different configurations, to realize the state transition once the photoinduced defects appear during subsequent operation and dynamic capture for continuous renewal of defects. Consequently, spiropyrans work as light-triggered and self-healing sustainable passivation sites to realize continuous defect repair. The target devices retain 93% and 99% of their initial power conversion efficiencies after 456 h aging under ultraviolet illumination and 1200 h aging under full-spectrum illumination, respectively. This work provides a novel concept of sustainable passivation strategy to realize continuous defect-passivation and film-healing in perovskite photovoltaics.

Visualizing the Surface Photocurrent Distribution in Perovskite Photovoltaics.

Defect states play an important role in the photovoltaic performance of metal halide perovskites. Particularly, the passivation of surface defects has made great contributions to high-performance perovskite photovoltaics. This highlights the importance of understanding the surface defects from a fundamental level by developing more accurate and operando characterization techniques. Herein, a strategy to enable the surface carriers and photocurrent distributions on perovskite films to be visualized in the horizontal direction is put forward. The visual image of photocurrent distribution is realized by combining the static local distribution of carriers provided by scanning near-field optical microscopy with the dynamic transporting of carriers achieved via a scanning photocurrent measurement system. Taking a surface passivated molecule as an example, a comprehensive defect scene including static and dynamic as well as local and entire conditions is obtained using this strategy. The comprehensive analysis of the trap states in perovskite films is pioneered vertically and horizontally, which will powerfully promote the deep understanding of defect mechanisms and carrier behavior for the goal of fabricating high-performance perovskite optoelectronic devices.

Full-Dimensional Grain Boundary Stress Release for Flexible Perovskite Indoor Photovoltaics.

Perovskite photovoltaics are strong potential candidates to drive low-power off-grid electronics for indoor applications. Compared with rigid devices, flexible perovskite devices can provide a more suitable surface for indoor small electronic devices, enabling them have a broader indoor application prospect. However, the mechanical stability of flexible perovskite photovoltaics is an urgent issue solved. Herein, a kind of 3D crosslinking agent named borax is selected to carry out grain boundary penetration treatment on perovskite film to realize full-dimensional stress release. This strategy improves the mechanical and phase stabilities of perovskite films subjected to external forces or large temperature changes. The fabricated perovskite photovoltaics deliver a champion power conversion efficiency (PCE) of 21.63% under AM 1.5G illumination, which is the highest one to date. The merit of low trap states under weak light makes the devices present a superior indoor PCE of 31.85% under 1062 lux (LED, 2956 K), which is currently the best flexible perovskite indoor photovoltaic device. This work provides a full-dimensional grain boundary stress release strategy for highly stable flexible perovskite indoor photovoltaics.

The DmeRF System Is Involved in Maintaining Cobalt Homeostasis in Vibrio parahaemolyticus.

Although cobalt (Co) is indispensable for life, it is toxic to cells when accumulated in excess. The DmeRF system is a well-characterized metal-response system that contributes to Co and nickel resistance in certain bacterial species. The Vibrio parahaemolyticus RIMD 2210633 genome also harbors a dmeRF operon that encodes a multiple antibiotic resistance regulator family transcriptional regulator and a cation diffusion facilitator family protein. Quantitative real-time PCR, growth curves analysis, inductively coupled plasma-mass spectrometry, ß-galactosidase activity assays, electrophoretic mobility shift assays, and a mouse infection experiment were performed to characterize the function of the DmeRF system in V. parahaemolyticus. Zinc, copper, and Co significantly increase dmeF expression, with Co inducing the greatest increase. DmeF promotes V. parahaemolyticus growth under high-Co conditions. Additionally, increased accumulation of cellular Co in the ΔdmeF mutant indicates that DmeF is potentially involved in Co efflux. Moreover, DmeR represses the dmeRF operon by binding directly to its promoter in the absence of Co. Finally, the DmeRF system was not required for V. parahaemolyticus virulence in mice. Collectively, our data indicate that the DmeRF system is involved in maintaining Co homeostasis in V. parahaemolyticus and DmeR functioning as a repressor of the operon.

Randomized Controlled Trial Comparing the Short-term Outcomes of Enhanced Recovery After Surgery and Conventional Care in Laparoscopic Distal Gastrectomy (GISSG1901).

OBJECTIVE: This study aimed to compare the effects of ERAS and conventional programs on short-term outcomes after LDG. SUMMARY OF BACKGROUND DATA: Currently, the ERAS program is broadly applied in surgical areas. Although several benefits of LDG with the ERAS program have been covered, high-level evidence is still limited, specifically in advanced gastric cancer. METHODS: The present study was designed as a randomized, multicenter, unblinded trial. The enrollment criteria included histologically confirmed cT2-4aN0-3M0 gastric adenocarcinoma. Postoperative complications, mortality, readmission, medical costs, recovery, and laboratory outcomes were compared between the ERAS and conventional groups. RESULTS: Between April 2019 and May 2020, 400 consecutive patients who met the enrollment criteria were enrolled. They were randomly allocated to either the ERAS group (n = 200) or the conventional group (n = 200). After excluding patients who did not undergo surgery or gastrectomy, 370 patients were analyzed. The patient demographic characteristics were not different between the 2 groups. The conventional group had a significantly longer allowed day of discharge and postoperative hospital stay (6.96 vs 5.83 days, P < 0.001; 8.85 vs 7.27 days, P < 0.001); a longer time to first flatus, liquid intake and ambulation (3.37 vs 2.52 days, P < 0.001; 3.09 vs 1.13 days, P < 0.001; 2.85 vs 1.38 days, P < 0.001, respectively); and higher medical costs (6826 vs 6328 $, P = 0.027) than the ERAS group. Additionally, patients in the ERAS group were more likely to initiate adjuvant chemotherapy earlier (29 vs 32 days, P = 0.035). There was no significant difference in postoperative complications or in the mortality or readmission rates. Regarding laboratory outcomes, the procalcitonin and C-reactive protein levels on postoperative day 3 were significantly lower and the hemoglobin levels on postoperative day 5 were significantly higher in the ERAS group than in the conventional group. CONCLUSION: The ERAS program provides a faster recovery, a shorter postoperative hospitalization length, and lower medical costs after LDG without increasing complication and readmission rates. Moreover, enhanced recovery in the ERAS group enables early initiation of adjuvant chemotherapy.

Acid modification enhances selective catalytic reduction activity and sulfur dioxide resistance of manganese-cerium-cobalt catalysts: Insight into the role of phosphotungstic acid.

Improving the SO2 resistance of catalysts is crucial to driving commercial applications of Mn-based catalysts. In this work, the phosphotungstic acid (HPW) modification strategy was applied to improve the N2 selectivity, SO2 and H2O resistance of the Mn-Ce-Co catalyst, and further, the mechanism of HWP modification on enhanced catalytic performance was explored. The results showed that HPW-Mn-Ce-Co catalyst exhibits higher NOx conversion (~100% at 100-250 °C) and N2 selectivity (exceed 80% at 50-350 °C) due to more oxygen vacancies, greater surface acidity, and lower redox capacity. In situ diffused reflectance infrared Fourier transform spectroscopy (in situ DRIFTS) reveal that HPW changed the reaction path of Mn-Ce-Co catalysts, promoted the adsorption and activation of NH3, and reduced the effect of SO2 on the active bidentate nitrate species, and thereby exhibiting good SO2 resistance. X-ray photoelectron spectrometer (XPS) and NH3 temperature-programmed desorption of (NH3-TPD) results show that HPW can inhibit the formation of metal sulfate, and SO2 can be combined with Ce species more easily. The generated Ce2(SO3)3 can not only protect Mn species but also increase the acid sites and weaken the poisoning effect of metal sulfate. This study provides a simple design strategy for the catalyst to improve the low-temperature catalytic performance and toxicity resistance.

TLR4 signalling via Piezo1 engages and enhances the macrophage mediated host response during bacterial infection.

TLR4 signaling plays key roles in the innate immune response to microbial infection. Innate immune cells encounter different mechanical cues in both health and disease to adapt their behaviors. However, the impact of mechanical sensing signals on TLR4 signal-mediated innate immune response remains unclear. Here we show that TLR4 signalling augments macrophage bactericidal activity through the mechanical sensor Piezo1. Bacterial infection or LPS stimulation triggers assembly of the complex of Piezo1 and TLR4 to remodel F-actin organization and augment phagocytosis, mitochondrion-phagosomal ROS production and bacterial clearance and genetic deficiency of Piezo1 results in abrogation of these responses. Mechanistically, LPS stimulates TLR4 to induce Piezo1-mediated calcium influx and consequently activates CaMKII-Mst1/2-Rac axis for pathogen ingestion and killing. Inhibition of CaMKII or knockout of either Mst1/2 or Rac1 results in reduced macrophage bactericidal activity, phenocopying the Piezo1 deficiency. Thus, we conclude that TLR4 drives the innate immune response via Piezo1 providing critical insight for understanding macrophage mechanophysiology and the host response.

Evolution mechanism of transition metal in NH3-SCR reaction over Mn-based bimetallic oxide catalysts: Structure-activity relationships.

The unexpected phenomenon in which different transition metals (Co, Ni and Cu) presented significant variation of participation levels as the auxiliaries in Mn-based bimetallic oxide catalysts were reported here. It is found that the Co element more easily to form Mn enriched surface bimetallic oxides with Mn than Ni and Cu, resulting in Co-MnOx exhibited the best deNOx activity and SO2 tolerance, followed by Ni-MnOx and Cu-MnOx. The role of different transition metal and structure-activity relationships were systematically investigated by advanced techniques including Synchrotron XAFS and in situ DRIFTs analysis. The excellent activity of Co-MnOx was related to its unique Mn-enriched surface (Co2+)tet(Mn3+ Co3+)octO4 structure with Mn cations occupying the octahedral sites, which is superior to the Ni-MnOx and Cu-MnOx with Mn-lean surface. In addition, the reaction energy barrier of Co-MnOx is weakened due to the lower electron cloud density around the Mn atom as compared to Ni-MnOx and Cu-MnOx. Moreover, Co-MnOx benefiting from the rapid electron migration between Mn and Co, more active bidentate/bridged nitrates could react with adsorbed NH3 in faster reaction rates following the L-H mechanism.

Role of Surgical Approach to Synchronous Colorectal Liver Metastases: A Retrospective Analysis.

PURPOSE: This study is a retrospective analysis of exploring the efficiency of surgical management on patients with synchronous colorectal liver metastasis (SCLM). PATIENTS AND METHODS: Nine hundred fifty-three consecutive patients with SCLM from Weifang People's Hospital of Shandong Province between January 2006 and December 2015 were reviewed. The values of different factors were analyzed, such as different surgical indications of liver metastases, simultaneous or staged resection of primary colorectal cancer and liver metastases, and primary tumor resection (PTR) of asymptomatic patients with unresectable liver metastases. RESULTS: Median survival time (47.3 months) and 5-year survival rate (31%) for patients with resected liver metastases were significantly superior to that of with nonoperative treatment (17.2 months, 4%, P<0.001); enlarging the standard of liver metastases resection can improve the resection rates (31.0% vs 13.6%, P<0.001); for patients with resectable liver metastases, the in-hospital cost for simultaneous resection group was lower than that in the staged resection group (36,698 vs 45,134 RMB, P<0.001); for patients of the asymptomatic primary tumor with unresectable liver metastases, PTR was associated with improved median survival (18.0 vs 15.0 months, P=0.006). CONCLUSION: For patients with SCLM, liver resection is considered the best treatment; expanding indications of liver resection can improve the resection rates. Simultaneous resection of the primary tumor and liver metastases were indicated in patients with resectable SCLM; PTR was recommended for asymptomatic patients with unresectable hepatic metastases.

Pd@Pt-GOx/HA as a Novel Enzymatic Cascade Nanoreactor for High-Efficiency Starving-Enhanced Chemodynamic Cancer Therapy.

Glucose oxidase (GOx)-mediated starvation therapy has demonstrated good application prospect in cancer treatment. However, the glucose- and oxygen-depletion starvation therapy still suffers from some limitations like low therapeutic efficiency and potential side effects to normal tissues. To overcome these disadvantages, herein a novel enzymatic cascade nanoreactor (Pd@Pt-GOx/hyaluronic acid (HA)) with controllable enzymatic activities was developed for high-efficiency starving-enhanced chemodynamic cancer therapy. The Pd@Pt-GOx/HA was fabricated by covalent conjugation of GOx onto Pd@Pt nanosheets (NSs), followed by linkage with hyaluronic acid (HA). The modification of HA on Pd@Pt-GOx could block the GOx activity, catalase (CAT)-like and peroxidase (POD)-like activities of Pd@Pt, reduce the cytotoxicity to normal cells and organs, and effectively target CD44-overexpressed tumors by active targeting and passive enhanced permeability and retention (EPR) effect. After endocytosis by tumor cells, the intracellular hyaluronidase (Hyase) could decompose the outer HA and expose Pd@Pt-GOx for the enzymatic cascade reaction. The GOx on the Pd@Pt-GOx could catalyze the oxidation of intratumoral glucose by O2 for cancer starvation therapy, while the O2 produced from the decomposition of endogenous H2O2 by the Pd@Pt with the CAT-like activity could accelerate the O2-dependent depletion of glucose by GOx. Meanwhile, the upregulated acidity and H2O2 content in the tumor region generated by GOx catalytic oxidation of glucose dramatically facilitated the pH-responsive POD-like activity of the Pd@Pt nanozyme, which then catalyzed degradation of the H2O2 to generate abundant highly toxic •OH, thereby realizing nanozyme-mediated starving-enhanced chemodynamic cancer therapy. In vitro and in vivo results indicated that the controllable, self-activated enzymatic cascade nanoreactors exerted highly efficient anticancer effects with negligible biotoxicity.