Biphasic Rapid Culture in Differential Diagnosis of Tuberculosis.

Context: Early intervention and treatment are key measures for tuberculosis (TB) prevention and control, making early, rapid, and accurate diagnostic methods crucial. The Liquid-solid (Biphasic) rapid cultures is a novel tool for the differential diagnosis of tuberculosis. Objective: The study intended to evaluate the value of the biphasic cultures by comparing it to the acid-fast staining and liquid cultures, which have been the traditional gold-standard technology, to determine its value in the diagnosis of TB. Design: The research team conducted an experimental study. Setting: The study took place at the Affiliated Wuxi Fifth Hospital of Jiangnan University in Wuxi, China. Participants: Participants were 221 patients with suspected pulmonary tuberculosis who had been admitted to the hospital between July 2020 and December 2021. Outcome Measures: Using three methods-liquid-solid (biphasic) culture, acid-fast staining, and mycobacterial growth indicator tube (MGIT) 960 liquid culture, the research team tested participants' sputum samples: (1) for sensitivity; (2) for time to positive culture results, and (3) for differential diagnosis. Results: The biphasic culture's sensitivity was significantly higher than that of acid-fast staining, (P = .0003), and no significant difference existed between it and the MGIT 960 liquid cultures. The biphasic cultures's mean time to positivity was significantly shorter than that of the MGIT 960 liquid culture at the intervals 11-20 d (P < .0001) and 21-35 days (P = .0001). Moreover, the biphasic cultures could preliminarily differentiate nontuberculous mycobacteria (NTM) from mycobacterium tuberculosis (MTB), which is a significant advantage in tuberculosis diagnosis. Conclusions: This study highlights the potential of a biphasic culture as a reliable tool for the rapid differential diagnosis of tuberculosis, with a faster detection cycle and a higher sensitivity than conventional methods. The biphasic cultures is a valuable addition to the tuberculosis diagnostic armamentarium and can help improve patients' outcomes by enabling earlier diagnosis and treatments.

The association of blood urea nitrogen to serum albumin ratio with short-term outcomes in Chinese patients with congestive heart failure: A retrospective cohort study.

BACKGROUND AND AIMS: Limited evidence exists on the prognostic outcomes of the blood urea nitrogen to serum albumin ratio (B/A ratio) in congestive heart failure (CHF), particularly in developing countries with scarce heart failure epidemiological data. We aimed to investigate the association between B/A ratio and short-term outcomes in Chinese patients with CHF. METHODS AND RESULTS: We included 1761 CHF patients with available B/A ratio data from a cohort of 2008 patients. Patients were categorized into three groups based on B/A ratio (low to high). The primary endpoint was death or readmission within 28 days, and the secondary endpoint was death or readmission within 90 days. We employed restricted cubic spline analysis, Cox proportional hazards regression, and Kaplan-Meier curves to evaluate the relationship between B/A ratio at admission and the endpoints. Even after adjusting for other variables, higher B/A ratios were associated with increased rates of 28 days and 90 days mortality or readmission (HR: 2.4, 95% CI: 1.81-3.18 and HR: 1.74, 95% CI: 1.48-2.05). Significant differences in the risks of both primary and secondary endpoints were observed among the three B/A ratio groups. The association between B/A ratio and CHF was stable in the different subgroups (all P for interaction＞0.05). CONCLUSION: Higher B/A ratios are associated with an increased risk of short-term mortality or readmission in Chinese patients with CHF. The B/A ratio shows promise as a prognostic indicator for short-term outcomes in CHF patients.

Adult zebrafish infected by clinically isolated Klebsiella pneumoniae with different virulence showed increased intestinal inflammation and disturbed intestinal microbial biodiversity.

BACKGROUND: Klebsiella pneumoniae is a pathogen that often infects patients in clinical practice. Due to its high virulent and drug resistance, infected patients are difficult to treat. In clinical practice, Klebsiella pneumoniae can infect patients' intestines, intestines, blood, etc., causing pathological changes. However, there is relatively little information on the impact of Klebsiella pneumoniae on intestinal inflammation and microbial populations. Zebrafish is an excellent biomedical model that has been successfully applied to the virulence assessment of Klebsiella pneumoniae. METHODS: In this study, three clinically isolated representative strains of Klebsiella pneumoniae (high virulence non-resistant, high virulence resistant, and low virulence resistant) were used to infect zebrafish, and their effects on intestinal colonization, inflammation, pathology, and microbial diversity were tested. RESULTS: Enzyme-linked immunoassay (ELISA) showed that Klebsiella pneumoniae significantly increased levels of the cytokines interleukin-1α (Il-1α), interleukin-1ß (Il-1ß), and tumor necrosis factor-α (Tnf-α), which increased inflammatory symptoms. Hematoxylin eosin staining(H&S) showed that Klebsiella pneumoniae treatment caused intestinal lesions in zebrafish, in which KP1053 exposure significantly decreased the number of goblet cells, KP1195 caused epithelial dissolution and exfoliation. In addition, Klebsiella pneumoniae disturbed the composition of intestinal microbiota, and the Shannon index increased, which increased the number of harmful bacteria. CONCLUSIONS: Klebsiella pneumoniae infection can lead to intestinal colonization, inflammation, pathological changes, and changes in microbial biodiversity. This study provides a reference for the intestinal pathology of clinical Klebsiella pneumoniae infection.

Robust and scalable single-molecule protein sequencing with fluorosequencing.

The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications.

Analysis of the effect of anti-tuberculosis therapy combined with all-in-one nursing care on the alleviation of inflammation in patients with pulmonary tuberculosis.

To analyze the application effect of anti-tuberculosis therapy (ATT) combined with all-in-one nursing care on pulmonary tuberculosis (PT). Seventy-four PT patients who received ATT in our hospital between December 2015 and June 2016 were selected as the research participants and randomized into a research group (RG; n=37) and a control group (CG; n=37) that were given all-in-one nursing care and routine care, respectively. The cure rate and treatment compliance were compared between groups, and the awareness of disease prevention and treatment was investigated. Patients' psychological status and quality of life were evaluated using the Self-Rating Depression/Anxiety Scale (SAS/SDS) and the Quality of Life Questionnaire Core 30 (QLQ-C30), respectively. RG and CG were not statistically different in the clinical cure rate (P>0.05), but the X-ray cure rate was higher and the recurrence rate was lower in RG (P<0.05). In addition, RG showed higher medication compliance rate, regular reexamination rate and awareness of disease prevention and treatment than CG (P<0.05). Reductions in SAS/SDS scores were observed in both groups after care, with even lower levels in RG, while the QLQ-C30 score increased and was higher in RG as compared to CG (P<0.05). Therefore, All-in-one nursing care can effectively enhance the level of treatment compliance and awareness of disease prevention and treatment of PT patients. In the future, when treating PT patients in the clinic, the effectiveness of ATT can be improved by implementing all-in-one nursing care to provide more reliable prognosis for patients.

Ordered deployment of distinct ciliary beating machines in growing axonemes of vertebrate multiciliated cells.

The beating of motile cilia requires the coordinated action of diverse machineries that include not only the axonemal dynein arms, but also the central apparatus, the radial spokes, and the microtubule inner proteins. These machines exhibit complex radial and proximodistal patterns in mature axonemes, but little is known about the interplay between them during motile ciliogenesis. Here, we describe and quantify the relative rates of axonemal deployment for these diverse cilia beating machineries during the final stages of differentiation of Xenopus epidermal multiciliated cells.

Neutrophil membrane-coated nanoparticles exhibit increased antimicrobial activities in an anti-microbial resistant K. pneumonia infection model.

OBJECTIVE: To investigate the efficacy and safety of neutrophil membrane-coated nanoparticles mediated KLA peptides (KLAKLAKKLAKLAK) and gentamicin in the targeted therapy of anti-microbial resistant Klebsiella pneumoniae (K. pneumonia) lung infection. METHODS: The characteristics of KLA-neutrophils nanoparticles (NNPs) are identified via dynamic light scattering (DLS), transmission electron microscope (TEM), SDS-PAGE, Western blot, quantitative flow cytometry (QFCM) and confocal microscopy. The safety of KLA-NNPs both in vitro and in vivo is evaluated by hemolysis test, platelet α granule membrane protein concentration, protein adsorption capacity, in vitro macrophage phagocytosis, weight change, liver function indicators, blood biochemical indicators, and pathological changes of vital organs in mice. The efficacy of KLA-NNPs is determined by time-kill assay, fluorescent label test, intracellular bacterial content, caspase-1 activity, survival rate, and HE staining both in vitro and in vivo. RESULTS: The prepared KLA-NNPs have a typical "core-shell" structure, uniform nanometer size, and retain the membrane proteins on the neutrophil membrane that achieve functional effects. In vitro safety analysis showed that KLA-NNPs have good blood compatibility and can inhibit macrophage phagocytosis in vitro. KLA-NNPs can effectively release KLA and significantly reduce intracellular bacteria and caspase-1 activity. In vivo safety analysis and efficacy analysis revealed that KLA-NNPs have good biocompatibility and could effectively improve the survival rate of mice. CONCLUSION: The prepared KLA-NNPs have good nano-medicine chemical and physical properties and safety. It can evade immune system clearance, achieve high-efficiency targeted aggregation and drug delivery to bacterial infection sites, and effectively inhibit the development of pneumonia induced by drug-resistant K. pneumonia.

Klebsiella pneumoniae activates the TGF-ß signaling pathway to adhere to and invade intestinal epithelial cells via enhancing TLL1 expression.

Klebsiella pneumoniae is a gram-negative bacterium that can cause many diseases in hospitals and communities. Intestinal K. pneumoniae infections are relatively rare. Most K. pneumoniae infections begin with the colonization of the gastrointestinal system. In this study, clinically isolated K. pneumoniae strains were used to infect intestinal epithelial Caco-2 cells to study the possible intestinal translocation mechanism of K. pneumoniae. We found that of the three K. pneumoniae strains tested, KP1821 exhibited the strongest adhesive and invasive abilities and that the adhesion to Caco-2 intestinal epithelial cells was affected by the acidic environment of the stomach. Transcriptome sequencing revealed the involvement of molecules associated with the extracellular matrix and cell adhesion, inflammatory response, calcium ion and transforming growth factor ß (TGF-ß) signaling pathways, and other abnormalities in biological processes and cell signaling pathways. Additionally, tolloid-like protein 1 (TLL1) was significantly upregulated. Knocking down TLL1 with shRNA significantly reduced KP1821's ability to invade and adhere to intestinal epithelial cells. TLL1 is involved in the activation of the TGF-ß signaling pathway. Inhibition of this pathway using the inhibitor SB431542 induced significantly reduced adhesion and invasion capabilities of KP1821. Our findings demonstrate that TLL1 participates in K. pneumoniae adhesion and invasion of intestinal epithelial cells by activating the TGF-ß signaling pathway.

Functionalized Erythrocyte Membrane-Coated Nanoparticles for the Treatment of Klebsiella pneumoniae-Induced Sepsis.

Sepsis is a systemic inflammatory response syndrome caused by infection, with high incidence and mortality. Therefore, it is necessary to carry out an effective anti-infection treatment. In this work, we designed and synthesized red blood cell (RBC) membrane-coated PLGA nanoparticles named γ3-RBCNPs, which target the highly expressed intercellular adhesion molecule-1 (ICAM-1) at the site of infection through the γ3 peptide on its surface and kill the Klebsiella pneumoniae through ciprofloxacin encapsulated in its core. In addition, the homogenous RBC membrane coated on the surface of the nanoparticles helps them avoid immune surveillance and prolong the circulation time of the drug in the body. We found that the γ3-RBCNPs target human umbilical vein endothelial cells (HUVECs) activated by TNF-α in vitro and the infected lung of mice in the sepsis model very well. In vitro evaluation suggested that γ3-RBCNPs have a low risk of acute hemolysis and are less likely to be engulfed by macrophages. In vivo evaluation showed that γ3-RBCNPs has a long half-life and good bio-safety. More importantly, we confirmed that γ3-RBCNPs have the good antibacterial and anti-infection ability in vivo and in vitro. Our research provides a new strategy for the nano-drug treatment of Klebsiella pneumoniae-induced sepsis.

Evaluation of droplet digital PCR rapid detection method and precise diagnosis and treatment for suspected sepsis (PROGRESS): a study protocol for a multi-center pragmatic randomized controlled trial.

BACKGROUND: Sepsis is still a major public health concern and a medical emergency due to its high morbidity and mortality. Accurate and timely etiology diagnosis is crucial for sepsis management. As an emerging rapid and sensitive pathogen detection tool, digital droplet PCR (ddPCR) has shown promising potential in rapid identification of pathogens and antimicrobial resistance genes. However, the diagnostic value and clinical impact of ddPCR tests remains to be studied in patients with suspected sepsis. PROGRESS trial is aimed to evaluate the clinical effectiveness of a novel ddPCR assay compared with standard practice. METHODS: PROGRESS is a multicenter, open-label, pragmatic randomized controlled trial (pRCT) set in ten hospitals, including departments of infectious disease and intensive care units. In this study, a total of 2292 patients with suspected sepsis will be randomly assigned to two arms: the ddPCR group and the control group with a ratio of 3:1. The primary outcome is the diagnostic efficacy, that is, the sensitivity and specificity of the ddPCR assay compared with the synchronous blood culture. Secondary outcomes include the mortality rates and the mean Sequential Organ Failure Assessment (SOFA) score at follow-up time points, the length of stay in the hospital, the time to directed antimicrobial therapy, duration of broad-spectrum antibiotic use, and the EQ-5D-5L score on day 90. DISCUSSION: It is the first multicenter pragmatic RCT to explore the diagnostic efficacy and clinical impact of the ddPCR assay in patients with suspected sepsis, taking advantage of both RCT's ability to establish causality and the feasibility of pragmatic approaches in real-world studies (RWS). This trial will help us to get a comprehensive view of the assay's capacity for precise diagnosis and treatment of sepsis. It has the potential to monitor the pathogen load change and to guide the antimicrobial therapy, making a beneficial impact on the prognosis of sepsis patients. TRIAL REGISTRATION: ClinicalTrial.gov, NCT05190861. Registered January 13, 2022-'Retrospectively registered', https://clinicaltrials.gov/ct2/show/NCT05190861 .

Human neutrophil peptide 1 promotes immune sterilization in vivo by reducing the virulence of multidrug-resistant Klebsiella pneumoniae and increasing the ability of macrophages.

By studying the expression in patients and cell modeling in vitro, antimicrobial peptides for Klebsiella were screened. Killing curve and membrane permeability experiments are used to study the antibacterial effect of antimicrobial peptides in vitro. Cytotoxicity-related indicators including lipopolysaccharide (LPS), capsule polysaccharide (CPS), and outer membrane protein expression were measured. Intranasal inoculation of pneumoconiosis was used to construct a mouse infection model, and the survival rate and cytokine expression level were tested. Human neutrophil peptide 1 (HNP-1) showed a significant antibacterial effect, which improved the permeability of the outer membrane of K. pneumoniae. Moreover, HNP-1 decreased LPS, CPS content, and outer membrane proteins. K. pneumoniae infection decreased antimicrobial peptide, oxidative stress, and autophagy-related genes, while HNP-1 increased these genes. After coculture with macrophages, the endocytosis of macrophages is enhanced and the bacterial load is greater in the K. pneumoniae + peptide group. Besides, higher levels of pp38 and pp65 in the K. pneumoniae + peptide group. HNP-1 rescued the cytotoxicity induced by K. pneumoniae. The survival rate is significantly improved after K. pneumoniae is treated by HNP-1. All cytokines in the peptide group were significantly higher. HNP-1 promotes immune sterilization by reducing the virulence of multidrug-resistant K. pneumoniae and increasing the ability of macrophages.

Plasma exosome-derived fragile site-associated tumor suppressor as a powerful prognostic predictor for patients with ovarian cancer.

The objective of the study was to investigate the levels of plasma exosome-derived fragile site-associated tumor suppressor (FATS) and evaluate its prognostic predictive ability in ovarian cancer (OC) patients. Exosome-rich fractions were isolated from the plasma of 90 patients with OC enrolled in this study. The levels of plasma exosome-derived FATS were detected by ELISA. The levels of exosome-derived FATS in OC patients were significantly lower as compared to the healthy controls (P < 0.001). The levels of plasma exosome-derived FATS were higher in OC patients with low grade (1/2), and Federation International of Gynecology and Obstetrics (FIGO) Stages I/II than those in high grade (3/4) and Stages III/IV of the disease (p = 0.003; p < 0.001), respectively. The levels of plasma exosome-derived FATS were significantly higher in OC patients with no lymph node metastasis or no ascites as compared to those with lymph node metastasis or ascites, respectively (both p < 0.001). The levels of plasma exosome-derived FATS were higher in OC patients having CA-125 below 35 U/ml as compared to those with CA-125 greater than 35 U/ml (p < 0.001). Among all enrolled OC patients, both 5-DFS and 5-OS were shorter in patients with lower plasma exosome-derived FATS levels than those with higher levels (both p < 0.001). The area under the receiver operating characteristic curve of plasma exosome-derived FATS was 0.85 (95% CI: 0.76-0.91) for 5-DFS and 0.91 (95% CI: 0.83-0.96) for 5-OS prediction in patients with OC. Plasma exosome-derived FATS levels in OC patients were significantly downregulated. Low levels of plasma exosome-derived FATS had a significant relationship with FIGO Stages III/IV, high grade, ascites, higher levels of CA-125, lymph node metastasis, and prognosis of OC patients. Thus, our findings may provide insights for the development of a new strategy OC treatment.

Plasma exosome-derived B-cell translation gene 1: a predictive marker for the prognosis in patients with non-small cell lung cancer.

Objective: In this study, we wanted to investigate the plasma exosome-derived B-cell translocation gene 1 (BTG-1) level as a predictive marker for the prognosis in patients with Non-small cell lung cancer (NSCLC). Patients and Methods: The expression of BTG-1 protein and BTG-1 mRNA in NSCLC tissues and adjacent tissues of 98 enrolled patients were detected by immunohistochemistry (IHC), and RT-PCR. Exosome-rich fractions were isolated from the plasma of 262 NSCLC patients. ELISA was used to detect plasma exosome-derived BTG-1 levels to evaluate the predictive value for the prognosis in patients with NSCLC. Results: IHC staining showed that the positive expression rate of BTG-1 protein in NSCLC tissues was 58.16%, whereas that in adjacent tissues was 91.84%. RT-PCR showed that BTG-1 mRNA expression was significantly lower in NSCLC tissues than in adjacent tissues (52.04% vs 87.76%, P < 0.05). Moreover, low plasma exosome-derived BTG-1 levels were related to tumor diameter, stage, metastasis, the degree of tumor differentiation, and abnormal carcinoembryonic antigen (CEA) levels. Multivariate Cox regression analysis showed that both the disease-free survival (DFS) and overall survival (OS) were shorter in patients with low plasma exosome-derived BTG-1 level compared with patients with high plasma exosome-derived BTG-1 level. The AUROC of plasma exosome-derived BTG-1 for 3-year DFS and 3-year OS were 0.94(95% CI; 0.91-0.98) and 0.94(95% CI: 0.90-0.98), respectively. For 3-year DFS, plasma exosome-derived BTG-1 had a sensitivity 91.0% and a specificity 82.3% for 3-year DFS, and a sensitivity 81.7% and a specificity 93.0% for 3-year OS, respectively. Conclusions: Plasma exosome-derived BTG-1 may be a potential biomarker for the prognosis in patients with NSCLC.

Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes.

RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. Although recent studies have systematically identified individual RNA-binding proteins, their higher-order assembly into ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that more than 20% of known human protein complexes contain RNA. To explore the role of RNA in the assembly of each complex, we identify complexes that dissociate, change composition, or form stable protein-only complexes in the absence of RNA. We use our method to systematically identify cell-type-specific RNA-associated proteins in mouse embryonic stem cells and finally, distribute our resource, rna.MAP, in an easy-to-use online interface (rna.proteincomplexes.org). Our system thus provides a methodology for explorations across human tissues, disease states, and throughout all domains of life.

A liquid-like organelle at the root of motile ciliopathy.

Motile ciliopathies are characterized by specific defects in cilia beating that result in chronic airway disease, subfertility, ectopic pregnancy, and hydrocephalus. While many patients harbor mutations in the dynein motors that drive cilia beating, the disease also results from mutations in so-called dynein axonemal assembly factors (DNAAFs) that act in the cytoplasm. The mechanisms of DNAAF action remain poorly defined. Here, we show that DNAAFs concentrate together with axonemal dyneins and chaperones into organelles that form specifically in multiciliated cells, which we term DynAPs, for dynein axonemal particles. These organelles display hallmarks of biomolecular condensates, and remarkably, DynAPs are enriched for the stress granule protein G3bp1, but not for other stress granule proteins or P-body proteins. Finally, we show that both the formation and the liquid-like behaviors of DynAPs are disrupted in a model of motile ciliopathy. These findings provide a unifying cell biological framework for a poorly understood class of human disease genes and add motile ciliopathy to the growing roster of human diseases associated with disrupted biological phase separation.

Surface-Anchored Metal-Organic Frameworks as Versatile Resists for Gas-Assisted E-Beam Lithography: Fabrication of Sub-10 Nanometer Structures.

We demonstrate that surface-anchored metal-organic frameworks (SURMOFs) are extraordinary well-suited as resists for high-resolution focused electron beam induced processing (FEBIP) techniques. The combination of such powerful lithographic protocols with the huge versatility of MOF materials are investigated in respect to their potential in nanostructures fabrication. The applied FEBIP methods rely on the local decomposition of Fe(CO)5 and Co(CO)3NO as precursors, either by the direct impact of the focused electron beam (electron beam induced deposition, EBID) or through the interaction of the precursor molecules with preirradiated/activated SURMOF areas (electron beam induced surface activation, EBISA). We demonstrate the huge potential of the approach for two different types of MOFs (HKUST-1 and Zn-DPDCPP). Our "surface science" approach to FEBIP, yields well-defined deposits with each investigated precursor/SURMOF combination. Local Auger electron spectroscopy reveals clean iron deposits from Fe(CO)5; deposits from Co(CO)3NO contain cobalt, nitrogen, and oxygen. EBISA experiments were successful with Fe(CO)5. Remarkably EBISA with Co(CO)3NO does not result in deposit formation on both resists, making the process chemically selective. Most importantly we demonstrate the fabrication of "nested-L" test structures with Fe(CO)5 on HKUST-1 with extremely narrow line widths of partially less than 8 nm, due to reduced electron proximity effects within the MOF-based resists. Considering that the actual diameter of the electron beam was larger than 6 nm, we see a huge potential for significant reduction of the structure sizes. In addition, the role and high potential of loading and transport of the precursor molecules within the porous SURMOF materials is discussed.

Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function.

Multiciliated cells (MCCs) drive fluid flow in diverse tubular organs and are essential for the development and homeostasis of the vertebrate central nervous system, airway and reproductive tracts. These cells are characterized by dozens or hundreds of motile cilia that beat in a coordinated and polarized manner. In recent years, genomic studies have not only elucidated the transcriptional hierarchy for MCC specification but also identified myriad new proteins that govern MCC ciliogenesis, cilia beating and cilia polarization. Interestingly, this burst of genomic data has also highlighted that proteins with no obvious role in cilia do, in fact, have important ciliary functions. Understanding the function of proteins with little prior history of study presents a special challenge, especially when faced with large numbers of such proteins. Here, we define the subcellular localization in MCCs of ∼200 proteins not previously implicated in cilia biology. Functional analyses arising from the screen provide novel links between actin cytoskeleton and MCC ciliogenesis.

Localized growth of carbon nanotubes via lithographic fabrication of metallic deposits.

We report on the fabrication of carbon nanotubes (CNTs) at predefined positions and controlled morphology, for example, as individual nanotubes or as CNT forests. Electron beam induced deposition (EBID) with subsequent autocatalytic growth (AG) was applied to lithographically produce catalytically active seeds for the localized growth of CNTs via chemical vapor deposition (CVD). With the precursor Fe(CO)5 we were able to fabricate clean iron deposits via EBID and AG. After the proof-of-principle that these Fe deposits indeed act as seeds for the growth of CNTs, the influence of significant EBID/AG parameters on the deposit shape and finally the yield and morphology of the grown CNTs was investigated in detail. Based on these results, the parameters could be optimized such that EBID point matrixes (6 × 6) were fabricated on a silica surface whereby at each predefined site only one CNT was produced. Furthermore, the localized fabrication of CNT forests was targeted and successfully achieved on an Al2O3 layer on a silicon sample. A peculiar lift-up of the Fe seed structures as "flakes" was observed and the mechanism was discussed. Finally, a proof-of-principle was presented showing that EBID deposits from the precursor Co(CO)3NO are also very effective catalysts for the CNT growth. Even though the metal content (Co) of the latter is reduced in comparison to the Fe deposits, effective CNT growth was observed for the Co-containing deposits at lower CVD temperatures than for the corresponding Fe deposits.

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes.

Macromolecular protein complexes carry out many of the essential functions of cells, and many genetic diseases arise from disrupting the functions of such complexes. Currently, there is great interest in defining the complete set of human protein complexes, but recent published maps lack comprehensive coverage. Here, through the synthesis of over 9,000 published mass spectrometry experiments, we present hu.MAP, the most comprehensive and accurate human protein complex map to date, containing > 4,600 total complexes, > 7,700 proteins, and > 56,000 unique interactions, including thousands of confident protein interactions not identified by the original publications. hu.MAP accurately recapitulates known complexes withheld from the learning procedure, which was optimized with the aid of a new quantitative metric (k-cliques) for comparing sets of sets. The vast majority of complexes in our map are significantly enriched with literature annotations, and the map overall shows improved coverage of many disease-associated proteins, as we describe in detail for ciliopathies. Using hu.MAP, we predicted and experimentally validated candidate ciliopathy disease genes in vivo in a model vertebrate, discovering CCDC138, WDR90, and KIAA1328 to be new cilia basal body/centriolar satellite proteins, and identifying ANKRD55 as a novel member of the intraflagellar transport machinery. By offering significant improvements to the accuracy and coverage of human protein complexes, hu.MAP (http://proteincomplexes.org) serves as a valuable resource for better understanding the core cellular functions of human proteins and helping to determine mechanistic foundations of human disease.