Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping

Sequence libraries that cover all k-mers enable universal, unbiased measurements of binding to both oligonucleotides and peptides. While the number of k-mers grows exponentially in k, space on all experimental platforms is limited. Here, we shrink k-mer library sizes by using joker characters, which represent all characters in the alphabet simultaneously. We present the JokerCAKE (joker covering all k-mers) algorithm for generating a short sequence such that each k-mer appears at least p times with at most one joker character per k-mer. By running our algorithm on a range of parameters and alphabets, we show that JokerCAKE produces near-optimal sequences. Moreover, through comparison with data from hundreds of DNA-protein binding experiments and with new experimental results for both standard and JokerCAKE libraries, we establish that accurate binding scores can be inferred for high-affinity k-mers using JokerCAKE libraries. JokerCAKE libraries allow researchers to search a significantly larger sequence space using the same number of experimental measurements and at the same cost. We present a new compact sequence design that covers all k-mers utilizing joker characters and develop an efficient algorithm to generate such designs. We show through simulations and experimental validation that these sequence designs are useful for identifying high-affinity binding sites at significantly reduced cost and space. Keywords: sequence libraries; microarray design; de Bruijn graphNational Institutes of Health (U.S.) (Grant R01GM081871

Final results from a phase 2b randomized, placebo-controlled clinical trial of RBX2660: A microbiota-based drug for the prevention of recurrent Clostridioides difficile infection

INTRODUCTION: Effective treatments for recurrent Clostridioides difficile infection (rCDI) are urgently needed. RBX2660 is an investigational microbiota-based live biotherapeutic to reduce CDI recurrence following standard-of-care antibiotic treatment in individuals with rCDI. Here we report the final safety data through 24 months of follow-up as well as final efficacy data, reflecting alignment of the pre-specified statistical analysis plan definitions with the data presented. METHODS: The PUNCH CD2 clinical trial was a prospective, multicenter, randomized, double-blinded, placebo-controlled, three-arm phase 2b study conducted to evaluate the efficacy and safety of RBX2660 for the reduction of rCDI compared to placebo. Eligible patients were at least 18 years of age and had at least three episodes of CDI and at least two rounds of standard antibiotic treatment or had at least two episodes of severe CDI resulting in hospitalization. Patients were randomized 1:1:1 to group A, two doses of RBX2660; group B, two doses of placebo; or group C, one dose of RBX2660 and one dose of placebo; all administered 7 ± 2 days apart. Treatment success was prevention of recurrence, defined as absence of diarrhea and no re-treatment for CDI any time after the first dose until 8 weeks after the second dose of the study treatment. Safety was assessed by reports of adverse events and symptoms. The final efficacy and safety are reported for data available through 24 months. RESULTS: For the primary endpoint, treatment success at 8 weeks, 56.8% (25/45) of participants who received one dose of RBX2660 + one dose of placebo, 55.6% (25/45) of participants who received two doses of RBX2660, and 43.2% (19/44) of participants who received two doses of placebo in the final intention-to-treat (ITT) population were responders (both p = 0.2 vs placebo). In the per-protocol population, 87.5% (21/24) of participants who received one dose of RBX2660 + one dose of placebo and 58.1% (18/31) of those who received two doses of placebo had treatment success (p = 0.017; treatment difference, 29.4 [95% CI 7.6, 51.3]); 75.0% (21/28) of participants in the PP population who received two doses of RBX2660 were responders (p = 0.17 vs placebo). The safety profile of RBX2660, whether delivered as one or two doses, was similar to the placebo group. CONCLUSION: While the phase 2b PUNCH CD2 clinical trial did not meet its pre-defined primary endpoint of treatment success at 8 weeks after two doses of RBX2660 vs two doses of placebo, clinically meaningful data were obtained to justify proceeding with the single dose regimen in the phase 3 clinical trial, PUNCH CD3, now complete. To date, the cumulative data for RBX2660 demonstrate consistent efficacy and safety outcomes for reduction of CDI recurrence in adults. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov: NCT02299570

Similarities between structural distortions under pressure and chemical doping in superconducting BaFe2As2

The discovery of a new family of high Tc materials, the iron arsenides (FeAs), has led to a resurgence of interest in superconductivity. Several important traits of these materials are now apparent, for example, layers of iron tetrahedrally coordinated by arsenic are crucial structural ingredients. It is also now well established that the parent non-superconducting phases are itinerant magnets, and that superconductivity can be induced by either chemical substitution or application of pressure, in sharp contrast to the cuprate family of materials. The structure and properties of chemically substituted samples are known to be intimately linked, however, remarkably little is known about this relationship when high pressure is used to induce superconductivity in undoped compounds. Here we show that the key structural features in BaFe2As2, namely suppression of the tetragonal to orthorhombic phase transition and reduction in the As-Fe-As bond angle and Fe-Fe distance, show the same behavior under pressure as found in chemically substituted samples. Using experimentally derived structural data, we show that the electronic structure evolves similarly in both cases. These results suggest that modification of the Fermi surface by structural distortions is more important than charge doping for inducing superconductivity in BaFe2As2

Excited states of linear polyenes

We present density matrix renormalisation group calculations of the Pariser- Parr-Pople-Peierls model of linear polyenes within the adiabatic approximation. We calculate the vertical and relaxed transition energies, and relaxed geometries for various excitations on long chains. The triplet (3Bu+) and even- parity singlet (2Ag+) states have a 2-soliton and 4-soliton form, respectively, both with large relaxation energies. The dipole-allowed (1Bu-) state forms an exciton-polaron and has a very small relaxation energy. The relaxed energy of the 2Ag+ state lies below that of the 1Bu- state. We observe an attraction between the soliton-antisoliton pairs in the 2Ag+ state. The calculated excitation energies agree well with the observed values for polyene oligomers; the agreement with polyacetylene thin films is less good, and we comment on the possible sources of the discrepencies. The photoinduced absorption is interpreted. The spin-spin correlation function shows that the unpaired spins coincide with the geometrical soliton positions. We study the roles of electron-electron interactions and electron-lattice coupling in determining the excitation energies and soliton structures. The electronic interactions play the key role in determining the ground state dimerisation and the excited state transition energies.Comment: LaTeX, 15 pages, 9 figure

Linear and Nonlinear Optical constants of BiFeO_3

Using spectroscopic ellipsometry, the refractive index and absorption versus wavelength of the ferroelectric antiferromagnet Bismuth Ferrite, BiFeO_3 is reported. The material has a direct band-gap at 442 nm wavelength (2.81 eV). Using optical second harmonic generation, the nonlinear optical coefficients were determined to be d_15/d_22 = 0.20 +/- 0.01, d_31/d_22 = 0.35 +/- 0.02, d_33/d_22 = -11.4 +/- 0.20 and |d_22| = 298.4 +/- 6.1 pm/V at a fundamental wavelength of 800 nm.Comment: 4 pages, 3 figure

Large magneto-optical Kerr effect and imaging of magnetic octupole domains in an antiferromagnetic metal

When a polarized light beam is incident upon the surface of a magnetic material, the reflected light undergoes a polarization rotation. This magneto-optical Kerr effect (MOKE) has been intensively studied in a variety of ferro- and ferrimagnetic materials because it provides a powerful probe for electronic and magnetic properties as well as for various applications including magneto-optical recording. Recently, there has been a surge of interest in antiferromagnets (AFMs) as prospective spintronic materials for high-density and ultrafast memory devices, owing to their vanishingly small stray field and orders of magnitude faster spin dynamics compared to their ferromagnetic counterparts. In fact, the MOKE has proven useful for the study and application of the antiferromagnetic (AF) state. Although limited to insulators, certain types of AFMs are known to exhibit a large MOKE, as they are weak ferromagnets due to canting of the otherwise collinear spin structure. Here we report the first observation of a large MOKE signal in an AF metal at room temperature. In particular, we find that despite a vanishingly small magnetization of $M \sim$0.002 $\mu_{\rm B}$/Mn, the non-collinear AF metal Mn$_3$Sn exhibits a large zero-field MOKE with a polar Kerr rotation angle of 20 milli-degrees, comparable to ferromagnetic metals. Our first-principles calculations have clarified that ferroic ordering of magnetic octupoles in the non-collinear Neel state may cause a large MOKE even in its fully compensated AF state without spin magnetization. This large MOKE further allows imaging of the magnetic octupole domains and their reversal induced by magnetic field. The observation of a large MOKE in an AF metal should open new avenues for the study of domain dynamics as well as spintronics using AFMs.Comment: 30 pages, 4 figure

Planning Framework Options for The Massachusetts Ocean Plan (DRAFT)

The Massachusetts Ocean Partnership (MOP) Planning Frameworks Team, in consultation with the Massachusetts Executive Office of Energy and Environmental Affairs (EEA), and based on collective experience and a review of ocean, coastal and resource management programs from the US and other countries, suggests that nine elements are essential components of the framework for the Massachusetts Ocean Plan and its implementation. While management plans and programs generally have these elements in common, there are a range of options for carrying out each program component. These options were presented to structure and inform the development of the Massachusetts Ocean Plan. For the most part, the range of options represents those that were considered to be appropriate under the Commonwealth’s existing legal and administrative structure and responsive to the requirements of the Massachusetts Ocean Act. However, the general concepts these options represent are likely to be transferable to other jurisdictions (especially in the United States) and can inform future ocean management and planning in Massachusetts. Additionally, options or their core elements can be combined to create additional alternatives within one of the nine planning components

Histoplasmosis infection in patients with rheumatoid arthritis, 1998-2009

<p>Abstract</p> <p>Background</p> <p>Patients with rheumatic diseases including rheumatoid arthritis (RA) are at increased risk for infections related to both the disease and its treatments. These include uncommonly reported infections due to histoplasmosis.</p> <p>Methods</p> <p>Medical record review of all patients with a diagnosis of RA who developed new histoplasmosis infection in an endemic region between Jan 1, 1998 and Jan 30, 2009 and who were seen at Mayo Clinic in Rochester, Minnesota was performed.</p> <p>Results</p> <p>Histoplasmosis was diagnosed in 26 patients. Most patients were on combination therapies; 15 were on anti-tumor necrosis factor (anti-TNF) agents, 15 on corticosteroids and 16 on methotrexate. Most received more than 6 months of itraconazole and/or amphotericin treatment. Two patients died of causes unrelated to histoplasmosis. Anti-TNF treatment was restarted in 4/15 patients, with recurrence of histoplasmosis in one.</p> <p>Conclusions</p> <p>In this largest single center series of patients with RA and histoplasmosis in the era of immunomodulatory therapy, we found that most patients had longstanding disease and were on multiple immunomodulatory agents. Most cases were pulmonary; typical signs and symptoms of disease were frequently lacking.</p

Demographic gaps and requirements for participation: A systematic review of clinical trial designs in Hidradenitis Suppurativa

Background: Hidradenitis suppurativa (HS) is a chronic inflammatory disease that disproportionally affects women, as well as Black and biracial individuals. While adalimumab remains the only therapy approved by the Food and Drug Administration for HS, many HS clinical trials for novel and re-tasked therapies are ongoing or upcoming. To optimize treatment equity, reflect the patient population, and facilitate trial participation, it is important to elucidate aspects of clinical trial protocols that may systematically exclude specific patient groups or impose hardships. Objective: The study aimed to systematically review inclusion and exclusion criteria as well as participant demographics in HS clinical trials. Methods: A literature search of PubMed, Embase, Cochrane Central, and Web of Science databases was conducted. Peer-reviewed publications of randomized controlled trials that were written in English and had at least 10 participants were included. Title and abstract screening and data extraction were completed by two independent reviewers, with disagreements resolved by a third. Results: Twenty-three studies totaling 1,496 adult participants met the inclusion criteria. Race and ethnicity were not reported in 473/1,496 (31.6%) and 1,420/1,496 (94.9%) trial participants, respectively. Trial participants were predominantly white (811/1,023, 79.3%) and female (1,057/1,457, 72.5%). The median of each study’s average age was 35.7 years (IQR 33.5–38.0), and 17/23 (73.9%) trials excluded pediatric patients. Nearly all participants had Hurley Stage II (499/958, 52.0%) or Hurley Stage III (385/958, 40.2%) disease. Many trials excluded patients who were pregnant (19/23, 82.6%) and breastfeeding (13/23, 56.5%), or who had HS that was “too severe” (8/23, 34.8%) or “too mild” (16/23, 70.0%). Frequently, trial protocols required prolonged washout periods from HS therapies, relatively long duration in the study’s placebo arm, and prohibited concurrent analgesic use. Conclusions: This systematic review of 23 HS clinical trials totaling 1,496 participants identified substantial hardships imposed by trial participation, high rates of missing race and ethnicity data, and low representation of key patient groups, including those who identify as Black. Future trials with pragmatic study designs, broader inclusion criteria, and study sites in diverse communities may alleviate burdens of trial participation and improve enrollment of diverse patient groups