Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis.

RationaleThe monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment.ObjectiveWe utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy.MethodsSerum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points.ResultsA total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status.ConclusionA comprehensive host serum protein dataset reflective of TB treatment effect is defined. A repeating set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2, among others) were found to change significantly in response to treatment, to strongly correlate with culture status, and at baseline to be predictive of future culture conversion. If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care

Making Room for Zoom in Focus Group Methods: Opportunities and Challenges for Novice Researchers (During and Beyond COVID-19)

Als die COVID-19-Pandemie über die Welt hereinbrach, waren viele Menschen gezwungen, sich auf online-basierte Routinen einzustellen, darunter auch qualitative Forscher*innen, die nach alternativen Möglichkeiten zur Erhebung aussagekräftiger Daten suchten. Während Fokusgruppen traditionell Face to Face durchgeführt werden, bieten Fortschritte bei Online-Videokonferenzanwendungen neue Methoden zur Datenerhebung, die jedoch bisher nur selten untersucht wurden. In diesem Artikel berichten wir über die Erfahrungen von 12 Doktorand*innen mit der Durchführung von Fokusgruppen unter Verwendung von Zoom im Rahmen eines Kurses zu qualitativen Interviewmethoden. Wir reflektieren Chancen und Herausforderungen, die wir als Moderator*innen und Teilnehmer*innen bei der Nutzung von Zoom erlebten z.B. bei der Vorbereitung oder in Bezug auf Rapport, die Einbindung anderer digitaler Tools und von Internetverbindungen. Zusammenfassend lässt sich sagen, dass die Durchführung von Online-Fokusgruppen unter Verwendung von Zoom insgesamt eine positive Erfahrung war und mit Face-to-Face-Fokusgruppen vergleichbar ist. Möglichkeiten der Teilnehmer*innenrekrutierung, die Sicherheitsmerkmale von Zoom und die Nutzung von Zoom und allgemeiner neuen Technologien sollten auch jenseits der Pandemie weiter erforscht werden.As the COVID-19 pandemic swept through the world, it forced many people to adapt to an online-based routine, including qualitative researchers looking for alternative ways to collect meaningful data. While focus groups are traditionally conducted in-person, advances with online videoconferencing applications present a new method to collect data, however, few studies have explored this. In this article we present 12 doctoral students' experiences with conducting focus groups using the videoconferencing application Zoom during a qualitative methods course on interviewing methods. Through this self-study qualitative analysis, participants reflected on the opportunities and challenges experienced as both moderators and participants using Zoom including: preparation, rapport, incorporating other digital tools, and internet connectivity. In conclusion, doing focus groups online using Zoom was a positive experience overall and comparable to in-person focus groups for collecting qualitative data, despite the introduction of technology. More research on participant recruitment, new technology, Zoom's security features, and Zoom's use outside of a pandemic should be further explored

Measuring the mass of the central black hole in the bulgeless galaxy ngc 4395 from gas dynamical modeling

NGC 4395 is a bulgeless spiral galaxy, harboring one of the nearest known type 1 Seyfert nuclei. Although there is no consensus on the mass of its central engine, several estimates suggest it is one of the lightest massive black holes (MBHs) known. We present the first direct dynamical measurement of the mass of this MBH from a combination of two-dimensional gas kinematic data, obtained with the adaptive optics assisted near-infrared integral field spectrograph Gemini/NIFS and high-resolution multiband photometric data from Hubble Space Telescope's Wide Field Camera 3. We use the photometric data to model the shape and stellar mass-to-light ratio of the nuclear star cluster (NSC). From the Gemini/NIFS observations, we derive the kinematics of warm molecular hydrogen gas as traced by emission through the H2 1–0 S(1) transition. These kinematics show a clear rotational signal, with a position angle orthogonal to NGC 4395's radio jet. Our best-fitting tilted ring models of the kinematics of the molecular hydrogen gas contain a black hole with mass M={4}-3+8× {10}5 M⊙ (3σ uncertainties) embedded in an NSC of mass M=2× {10}6 M⊙. Our black hole mass measurement is in excellent agreement with the reverberation mapping mass estimate of Peterson et al. but shows some tension with other mass measurement methods based on accretion signals

Stem diameter and rotational stability in revision total hip arthroplasty: a biomechanical analysis

BACKGROUND: Proximal femoral bone loss during revision hip arthroplasty often requires bypassing the deficient metaphyseal bone to obtain distal fixation. The purpose of this study was to determine the effect of stem diameter and length of diaphyseal contact in achieving rotational stability in revision total hip arthroplasty. METHODS: Twenty-four cadaveric femoral specimens were implanted with a fully porous-coated stem. Two different diameters were tested and the stems were implanted at multiple contact lengths without proximal bone support. Each specimen underwent torsional testing to failure and rotational micromotion was measured at the implant-bone interface. RESULTS: The larger stem diameter demonstrated a greater torsional stability for a given length of cortical contact (p ≤ 0.05). Decreasing length of diaphyseal contact length was associated with less torsional stability. Torsional resistance was inconsistent at 2 cm of depth. CONCLUSION: Larger stem diameters frequently used in revisions may be associated with less diaphyseal contact length to achieve equivalent rotational stability compared to smaller diameter stems. Furthermore, a minimum of 3 cm or 4 cm of diaphyseal contact with a porous-coated stem should be achieved in proximal femoral bone deficiency and will likely be dependent on the stem diameter utilized at the time of surgery

Effect of Thermal Phase Fluctuations on the Inductances of Josephson Junctions, Arrays of Junctions, and Superconducting Films

We calculate the factor by which thermal phase fluctuations, as distinct from phase-slip fluctuations, increase the inductance, LJ, of a resistively-shunted Josephson junction (JJ) above its mean-field value, L0. We find that quantum mechanics suppresses fluctuations when T drops below a temperature, TQ = h/kBGL0, where G is the shunt conductance. Examination of the calculated sheet inductance, LA(T)/L0(T), of arrays of JJ's reveals that 2-D interconnections halve fluctuation effects, while reducing phase-slip effects by a much larger factor. Guided by these results, we calculate the sheet inductance, LF(T)/L0(T), of 2-D films by treating each plasma oscillation mode as an overdamped JJ. In disordered s-wave superconductors, quantum suppression is important for LF(0)/LF(T) > 0.14, (or, T/TC0 < 0.94). In optimally doped YBCO and BSCCO quantum suppression is important for l2(0)/l2(T) > 0.25, where l is the penetration depth.Comment: 15 pages; 4 figures. Submitted to Physical Review B, May 199

A Modular BAM Complex in the Outer Membrane of the α-Proteobacterium Caulobacter crescentus

Mitochondria are organelles derived from an intracellular α-proteobacterium. The biogenesis of mitochondria relies on the assembly of β-barrel proteins into the mitochondrial outer membrane, a process inherited from the bacterial ancestor. Caulobacter crescentus is an α-proteobacterium, and the BAM (β-barrel assembly machinery) complex was purified and characterized from this model organism. Like the mitochondrial sorting and assembly machinery complex, we find the BAM complex to be modular in nature. A ∼150 kDa core BAM complex containing BamA, BamB, BamD, and BamE associates with additional modules in the outer membrane. One of these modules, Pal, is a lipoprotein that provides a means for anchorage to the peptidoglycan layer of the cell wall. We suggest the modular design of the BAM complex facilitates access to substrates from the protein translocase in the inner membrane

Genome Sequences of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, DarthP, Hammy, Krueger, LastHope, Peanam, PhelpsODU, Phrank, SirPhilip, Slimphazie, and Unicorn

We report the genome sequences of 14 cluster K mycobacteriophages isolated using Mycobacterium smegmatis mc2155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites

Genome-enabled insights into the biology of thrips as crop pests

Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species