Abstract: Systems, compositions, and methods for isolating HLA-peptides from cells. A universal platform and methods for profiling the HLA-peptidome, enabling identification of endogenously presented HLA-peptides from cell lines expressing any possible class I or II construct.

Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.

Abstract: T cell receptor (TCR) diversity of a subject, including TCR diversity in CD8+ T cell subsets, is used as a predictive indicator of responsiveness of the subject to cancer immunotherapy prior to initiation of the immunotherapy. Exemplified immunotherapy comprises administering an immune checkpoint inhibitor to a subject, wherein a TCR diversity value in CD8+ T cell subsets from the subject, such as CD8+ T cell subpopulations defined by differential cell surface marker expression, is higher than a reference value.

Abstract: This document provides methods and materials for identifying metastatic malignant skin lesions (e.g., malignant pigmented skin lesions). For example, methods and materials for using quantitative PCR results and correction protocols to reduce the impact of basal keratinocyte contamination on the analysis of test sample results to identify metastatic malignant skin lesions are provided. This document also provides methods and materials for treating skin cancer. For example, methods and materials for identifying a mammal (e.g., a human) having a pre-metastatic skin lesion (e.g., pre-metastatic melanoma) and treating that mammal with pentamidine (4,4?-[pentane-1,5-diylbis(oxy)]dibenzenecarboximidamide) are provided.

Abstract: Described are methods and systems for the treatment of individuals having a disorder characterized by complement system dysregulation. The described methods and systems may be used for a variety of purposes, including for example, establishing one or both of a general or personalized dosing schedule for treatment using a complement inhibitor, establishing a dosage schedule sufficient to maintain an effective amount of complement inhibitor, establishing general dosing schedules for novel complement modifying agents and identifying a treatment regimen and/or dose eliminating the possibility of under dosing medication, and treatment regimen and/or dose for reducing or preventing toxicity in a patient.

Abstract: This invention provides a primer used for a next-generation sequencer that can provide a large number of reads. On the basis of the sequence: 5?-CAAGCAGAAGACGGCATACGAGAT-N5 to 15-GTCTCGTGGGCTCGGAGATGTGTATAAGA-GACAG-3?, wherein N5 to 15 indicates an index sequence of 5 to 15 nucleotides), an index sequence is designed as a nucleotide sequence exhibiting the putative number of reads, which is calculated using the estimation formula designating the number of reads as a purpose variable and the type of nucleotides in the index sequence as an explanatory variable, exceeding a given level.

Abstract: Markers useful for determining multiple sclerosis activity in a human subject are provided, along with kits for measuring quantitative expression values of the markers. Also provided are computer systems and software embodiments of predictive models for scoring and determining multiple sclerosis activity in human subjects based on the quantitative expression values of the markers.

Abstract: Methods and systems for assessing the risk of a human subject for developing colorectal cancer are provided. These methods may be combined with the subject's clinical risk to improve risk analysis. Such methods may be used to assist decision making about appropriate colorectal cancer screening regimens.

Abstract: Processes, as well as associated systems and computer program (software) products, are disclosed for the biological conversion of CO into desired end products such as ethanol. The control methodologies used for these processes can advantageously result in a reduced time required for a batch operation or other initial operating period, prior to achieving a continuous operation, which may be demarcated either by the addition of fresh culture medium at a defined flow rate or by another process initiation target. The control methodologies may alternatively, or in combination, improve a process performance parameter, such as productivity of the desired end product or bacterial growth rate, during this batch operation or other initial operating period.

Abstract: A method for identifying a pathogen contained in a metagenomic sample and for identifying pathogenic markers in the genome of the pathogen includes: processing the sample to extract DNA from pathogens, sequencing the extracted DNA, thereby producing a set of reads, comparing the reads to a database of genomes of known pathogens to assign reads to the pathogens; producing a pool of reads and assembling them to produce contigs, comparing the contigs to a second database of markers to check whether they contain a marker. The method further includes the step of comparing the reads to the second database to assign reads to the markers, a read being assigned to a marker if it falls entirely into or is astride the marker, and the pool also includes the reads assigned to the markers, the contigs thereby being assembled from reads assigned to a pathogen and reads assigned to markers.

Abstract: The present invention is directed to the field of phage therapy for the treatment and control of bacterial infections, in particular respiratory bacterial infections such as bacterial pneumonia. More specifically, the present invention is directed to novel bacteriophage strains, and products and cocktails thereof, including F99/10, F110/10, F27/12, Psa_F83/13, Psa_F95/13, F391/08, Kle_F92/15, Kle_F105/15, Kle_F134/15, Kle_F141/15, as well as variants thereof; and methods of using same in the treatment and prevention of bacterial infections, including respiratory infections caused by, e.g., Pseudomonas aeruginosa and/or Klebsiella pneumoniae. The cocktails are used as pharmaceutical compositions either alone or in further combination with other therapies, e.g., antibiotics or other standard and non-standard therapies for respiratory infections.

Abstract: Compositions and methods for isolating HLA-peptides from cells. A universal platform and methods for profiling the HLA-peptidome, enabling identification of endogenously presented HLA-peptides from cell lines expressing any possible class I or II construct.

Abstract: A bioinformatics method for determining a risk score that indicates a risk that a subject will experience a negative clinical event within a certain period of time. The risk score is based on a combination of activities of two or more cellular signaling pathways in a subject, such as a human, wherein the specific cellular signaling pathways are the PI3K pathway and one or more of a Wnt pathway, an ER pathway, and an HH pathway. The invention also includes an apparatus with a digital processor configured to perform such a method, to a non-transitory storage medium storing instructions that are executable by a digital processing device to perform such a method, and to a computer program comprising program code means for causing a digital processing device to perform such a method. The invention achieves advanced prognosis of negative clinical events, for example, disease progression, recurrence, development of metastasis, or even death.

Abstract: A system for generating a genotypic causal model of a disease state includes a computing device that generates a causal graph containing genotypic causal nodes and connected symptomatic causal nodes, which contains causal paths from gene combinations to symptomatic datums. Genotypic causal nodes and/or connected symptomatic causal nodes may be generated by feature learning algorithms from training data.

Abstract: A bioinformatics method for determining a risk score that indicates a risk that a subject, in particular a human, will experience a negative clinical event within a certain period of time. The risk score is based on a unique combination of activities of two or more cellular signaling pathways in a subject, wherein the selected cellular signaling pathways are the TGF-? pathway and one or more of a PI3K pathway, a Wnt pathway, an ER pathway, and an HH pathway. The invention includes an apparatus with a digital processor configured to perform such a method, a non-transitory storage medium storing instructions that are executable by a digital processing device to perform such a method, and a computer program comprising program code means for causing a digital processing device to perform such a method.

Abstract: Systems and methods for rapid determination of microorganism growth and antimicrobial agent susceptibility and/or resistance are disclosed.

Abstract: Bifidobacterium longum strains and cell wall fractions isolated from Bifidobacterium longum strains are useful in the prophylaxis or treatment of a respiratory viral infection in a subject. They are also useful in the prophylaxis of a secondary bacterial infection associated with a respiratory viral infection in a subject, especially a subject who is susceptible to respiratory infections.

Abstract: Disclosed herein are methods for diagnosing acute cellular rejection (ACR) of an allograft by analysis of predictive gene sets and kits for practicing these methods.

Abstract: Cumulus cell (CC) gene expression is being explored as an additional method to morphological scoring to choose the embryo with the highest chance to pregnancy. The present invention relates to a novel method of identifying biomarker genes for evaluating the competence of a mammalian oocyte in giving rise to a viable pregnancy after fertilization, based on the use of live birth and embryonic development as endpoint criteria for the oocytes to be used in an exon level analysis of potential biomarker genes. The invention further provides CC-expressed biomarker genes thus identified, as well as prognostic models based on the biomarker genes identified using the methods of the present invention.