Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity

Background: Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the “twilight-” or “midnight– ” zones where pair-wise sequence identities to known sequences fall below 25 % and sequence-based functional annotations often fail. Results: Here we report a novel graph database mining method and demonstrate its application to protein structure pattern identification and structure classification. The biologic motivation of our study is to recognize common structure patterns in “immunoevasins”, proteins mediating virus evasion of host immune defense. Our experimental study, using both viral and non-viral proteins, demonstrates the efficiency and efficacy of the proposed method. Conclusions: We present a theoretic framework, offer a practical software implementation for incorporating prior domain knowledge, such as substitution matrices as studied here, and devise an efficient algorithm to identify approximate matched frequent subgraphs. By doing so, we significantly expanded the analytical power of sophisticated data mining algorithms in dealing with large volume of complicated and noisy protein structure data. And without loss of generality, choice of appropriate compatibility matrices allows our method to be easily employed in domains where subgraph labels have some uncertainty

Zoonotic orthopoxviruses encode a high-affinity antagonist of NKG2D

NK and T lymphocytes express both activating and inhibiting receptors for various members of the major histocompatibility complex class I superfamily (MHCISF). To evade immunologic cytotoxicity, many viruses interfere with the function of these receptors, generally by altering the displayed profile of MHCISF proteins on host cells. Using a structurally constrained hidden Markov model, we discovered an orthopoxvirus protein, itself distantly class I–like, that acts as a competitive antagonist of the NKG2D activating receptor. This orthopoxvirus MHC class I–like protein (OMCP) is conserved among cowpox and monkeypox viruses, secreted by infected cells, and bound with high affinity by NKG2D of rodents and humans (KD ∼ 30 and 0.2 nM, respectively). OMCP blocks recognition of host-encoded ligands and inhibits NKG2D-dependent killing by NK cells. This finding represents a novel mechanism for viral interference with NKG2D and sheds light on intercellular recognition events underlying innate immunity against emerging orthopoxviruses

Inadvertent Percutaneous Endoscopic Gastrostomy Tube Placement through the Transverse Colon to the Stomach Causing Intractable Diarrhea: A Case Report

Background. Among patients with chronic disease, percutaneous endoscopic gastrostomy (PEG) tubes are a common mechanism to deliver enteral feedings to patients unable to feed by mouth. While several cases in the literature describe difficulties with and complications of the initial placement of the PEG, few studies have documented the effects of a delayed diagnosis of a misplaced tube. Methods. This case study reviews the hospitalization of an 82 year old male with an inadvertent placement of a PEG tube through the transverse colon. Photos of the placement in the stomach as well as those of the follow up colonoscopy, and a recording of the episodes of diarrhea during the hospitalization were made. Results. The records of this patient reveal complaints of gastrointestinal distress and diarrhea immediately after placement of the tube. Placement in the stomach was verified by endoscopy, with discovery of the tube only after a follow up colonoscopy. The tube remained in place after this discovery, and was removed weeks after the diarrhea was unsuccessfully treated with antibiotics. After tube removal, the patient recovered well and was sent home

Effects of soybean lipid infusion on triglyceride and unbound free fatty acid levels in preterm infants

© 2018 Informa UK Limited, trading as Taylor & Francis Group Objective: To determine the plasma triglyceride (TG) and unbound free fatty acid (FFAu) levels in infants treated with increasing dosages of soybean lipid, intralipid (IL), infusion. Study design: TG and FFAu levels were measured in 78 preterm infants (BW 500–2000 g; GA 23–34 weeks) using the fluorescent probe ADIFAB2 and enzymatic method. Results: The infants’ BW was 1266.2 ± 440.7 g and GA 28.8 ± 3.1 weeks. TG levels were 77.4 ± 50 mg/dL, 140.2 ± 188 mg/dL (p \u3c .04 compared to levels during low dose IL infusion) and 135.6 ± 118 mg/dL (p \u3c .004), respectively during increased IL rates. FFAu levels were 17.7 ± 13 nM, 47.3 ± 102.8 nM (p = .07) and 98 ± 234 nM (p = .03). TG levels correlated with IL dose, the rate of IL administration, and FFAu levels. TG and FFAu levels were higher in infants below 28 weeks’ gestation Conclusions: Increasing dosage of IL is associated with increasing levels of TG and FFAu, especially in infants below 29 weeks of gestation. The increased level of FFAu suggests inefficient cellular utilization

User-Friendly MES Interfaces:Recommendations for an AI-Based Chatbot Assistance in Industry 4.0 Shop Floors

The purpose of this paper is to study an Industry 4.0 scenario of ‘technical assistance’ and use manufacturing execution systems (MES) to address the need for easy information extraction on the shop floor. We identify specific requirements for a user-friendly MES interface to develop (and test) an approach for technical assistance and introduce a chatbot with a prediction system as an interface layer for MES. The chatbot is aimed at production coordination by assisting the shop floor workforce and learn from their inputs, thus acting as an intelligent assistant. We programmed a prototype chatbot as a proof of concept, where the new interface layer provided live updates related to production in natural language and added predictive power to MES. The results indicate that the chatbot interface for MES is beneficial to the shop floor workforce and provides easy information extraction, compared to the traditional search techniques. The paper contributes to the manufacturing information systems field and demonstrates a human-AI collaboration system in a factory. In particular, this paper recommends the manner in which MES based technical assistance systems can be developed for the purpose of easy information retrieval

The Natural Selection of Herpesviruses and Virus-Specific NK Cell Receptors

During the co-evolution of cytomegalovirus (CMV) and natural killer (NK) cells, each has evolved specific tactics in an attempt to prevail. CMV has evolved multiple immune evasion mechanisms to avoid detection by NK cells and other immune cells, leading to chronic infection. Meanwhile, the host has evolved virus-specific receptors to counter these evasion strategies. The natural selection of viral genes and host receptors allows us to observe a unique molecular example of “survival of the fittest”, as virus and immune cells try to out-maneuver one another or for the virus to achieve détente for optimal dissemination in the population

Alliance or acquisition? A mechanisms‐based, policy‐capturing analysis

Research summary: While alliance researchers view prior partner‐specific alliance experience as influencing firms' subsequent alliance or acquisition decisions, empirical evidence on the alliance versus acquisition decision is surprisingly mixed. We offer a reconciliation by proposing and testing an analytical framework that recognizes prior partner‐specific experiences as heterogeneous along three fundamental dimensions: partner‐specific trust, routines, and value certainty. This allows us to use a policy‐capturing methodology to rigorously operationalize and test our mechanism‐level predictions. We find that all three mechanisms can increase the likelihood of a subsequent alliance or acquisition, and in terms of the comparative choice between alliances versus acquisitions, partner‐specific trust pulls towards alliances, and value certainty pulls towards acquisitions. We conclude with a discussion of the theoretical and empirical implications of our approach and method. Managerial summary: This study focuses on an important corporate decision: When a firm has had an alliance with another firm, how would that experience affect the likelihood of a future alliance or acquisition with that same firm? We first suggest that it will depend on three factors: the level of trust that existed in that prior alliance, the extent to which specific work routines were developed, and the degree to which the firm was able to confidently assess the value of the partner firm's resources. We then find that trust is a particularly strong predictor of future alliances, while confidence regarding value more strongly predicts future acquisitions. In this way, we demonstrate more precisely how past corporate choices can affect (consciously or unconsciously) future ones

High-dimensional analysis of the aging immune system: verification of age-associated differences in immune signaling responses in healthy donors.

BACKGROUND Single-cell network profiling (SCNP) is a multiparametric flow cytometry-based approach that simultaneously measures evoked signaling in multiple cell subsets. Previously, using the SCNP approach, age-associated immune signaling responses were identified in a cohort of 60 healthy donors. METHODS In the current study, a high-dimensional analysis of intracellular signaling was performed by measuring 24 signaling nodes in 7 distinct immune cell subsets within PBMCs in an independent cohort of 174 healthy donors [144 elderly (>65 yrs); 30 young (25-40 yrs)]. RESULTS Associations between age and 9 immune signaling responses identified in the previously published 60 donor cohort were confirmed in the current study. Furthermore, within the current study cohort, 48 additional immune signaling responses differed significantly between young and elderly donors. These associations spanned all profiled modulators and immune cell subsets. CONCLUSIONS These results demonstrate that SCNP, a systems-based approach, can capture the complexity of the cellular mechanisms underlying immunological aging. Further, the confirmation of age associations in an independent donor cohort supports the use of SCNP as a tool for identifying reproducible predictive biomarkers in areas such as vaccine response and response to cancer immunotherapies

New twist on the regulation of NKG2D ligand expression

The NK cell–activating receptor NKG2D plays a prominent role in antitumor immune responses. Expression of the multiple NKG2D ligands must be tightly controlled to guarantee that NK cells attack tumors but not healthy cells. New data reveal a novel mechanism of posttranslational regulation of the mouse NKG2D ligand MULT1, in which MULT1 is ubiquitinated and degraded in healthy cells. In response to UV stress or heat shock, ubiquitination of MULT1 decreases and cell surface expression increases. Thus, targeting the ubiquitination machinery in cancer cells might increase the susceptibility of tumors to NK cell–mediated killing