HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.

RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier (HydRA), which leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machines (SVMs), convolutional neural networks (CNNs), and Transformer-based protein language models. Occlusion mapping by HydRA robustly detects known RBDs and predicts hundreds of uncharacterized RNA-binding associated domains. Enhanced CLIP (eCLIP) for HydRA-predicted RBP candidates reveals transcriptome-wide RNA targets and confirms RNA-binding activity for HydRA-predicted RNA-binding associated domains. HydRA accelerates construction of a comprehensive RBP catalog and expands the diversity of RNA-binding associated domains.

Central 5-HTergic hyperactivity induces myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)-like pathophysiology.

OBJECTIVES: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a significant medical challenge, with no indisputable pathophysiological mechanism identified to date. METHODS: Based on clinical clues, we hypothesized that 5-hydroxytryptamine (5-HT) hyperactivation is implicated in the pathogenic causes of ME/CFS and the associated symptoms. We experimentally evaluated this hypothesis in a series of mouse models. RESULTS: High-dose selective serotonin reuptake inhibitor (SSRI) treatment induced intra- and extracellular serotonin spillover in the dorsal raphe nuclei of mice. This condition resulted in severe fatigue (rota-rod, fatigue rotating wheel and home-cage activity tests) and ME/CFS-associated symptoms (nest building, plantar and open field test), along with dysfunction in the hypothalamic-pituitary-adrenal (HPA) axis response to exercise challenge. These ME/CFS-like features induced by excess serotonin were additionally verified using both a 5-HT synthesis inhibitor and viral vector for Htr1a (5-HT1A receptor) gene knockdown. CONCLUSIONS: Our findings support the involvement of 5-HTergic hyperactivity in the pathophysiology of ME/CFS. This ME/CFS-mimicking animal model would be useful for understanding ME/CFS biology and its therapeutic approaches.

Structured illumination and image enhancement of three-dimensional and moving objects at a distance via incoherent Fourier ptychography.

We experimentally apply incoherent Fourier ptychography to enhance the resolution of recorded images by projecting known, uncorrelated, random patterns at high speed onto 3D moving and distant objects. We find that the resolution enhancement factor can be greater than 2, depending on the projection and camera optics.

Exploring optimal deep tunnel sewer systems to enhance urban pluvial flood resilience in the gangnam region, South Korea.

Urban pluvial flooding is becoming a global concern, exacerbated by urbanization and climate change, especially in rapidly developing areas where existing sewer systems lag behind growth. In order to minimize a system's functional failures during extreme rainfalls, localized engineering solutions are required for urban areas chronically suffering from pluvial floods. This study critically evaluates the Deep Tunnel Sewer System (DTSS) as a robust grey infrastructure solution for enhancing urban flood resilience, with a case study in the Gangnam region of Seoul, South Korea. To do so, we integrated a one-dimensional sewer model with a rapid flood spreading model to identify optimal routes and conduit diameters for the DTSS, focusing on four flood-related metrics: the total flood volume, the flood duration, the peak flooding rate, and the number of flooded nodes. Results indicate that, had the DTSS been in place, it could have reduced historical flood volumes over the last decade by 50.1-99.3%, depending on the DTSS route. Regarding the conduit diameter, an 8 m diameter was found to be optimal for minimizing all flood-related metrics. Our research also developed the Intensity-Duration-Frequency (IDF) surfaces in three dimensions, providing a correlation between simulated flood-related metrics and design rainfall characteristics to distinguish the effect of DTSS on flood risk reduction. Our findings demonstrate how highly engineered solutions can enhance urban flood resilience, but they may still face challenges during extreme heavy rainfalls with a 80-year frequency or above. This study contributes to rational decision-making and emergency management in the face of increasing urban pluvial flood risks.

Single pixel structured imaging through fog.

We describe the application of structured imaging with a single-pixel camera to imaging through fog. We demonstrate the use of a high-pass filter on the detected bucket signals to suppress the effects of temporal variations of fog density and enable an effective reconstruction of the image. A quantitative analysis and comparison of several high-pass filters are demonstrated for the application. Both computational ghost imaging and compressive sensing techniques were used for image reconstruction and compressive sensing was observed to give a higher reconstructed image quality.

Systematic review of randomized controlled trials for chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME).

BACKGROUND: Although medical requirements are urgent, no effective intervention has been proven for chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME). To facilitate the development of new therapeutics, we systematically reviewed the randomized controlled trials (RCTs) for CFS/ME to date. METHODS: RCTs targeting CFS/ME were surveyed using two electronic databases, PubMed and the Cochrane library, through April 2019. We included only RCTs that targeted fatigue-related symptoms, and we analyzed the data in terms of the characteristics of the participants, case definitions, primary measurements, and interventions with overall outcomes. RESULTS: Among 513 potentially relevant articles, 55 RCTs met our inclusion criteria; these included 25 RCTs of 22 different pharmacological interventions, 28 RCTs of 18 non-pharmacological interventions and 2 RCTs of combined interventions. These studies accounted for a total of 6316 participants (1568 males and 4748 females, 5859 adults and 457 adolescents). CDC 1994 (Fukuda) criteria were mostly used for case definitions (42 RCTs, 76.4%), and the primary measurement tools included the Checklist Individual Strength (CIS, 36.4%) and the 36-item Short Form health survey (SF-36, 30.9%). Eight interventions showed statistical significance: 3 pharmacological (Staphypan Berna, Poly(I):poly(C12U) and CoQ10 + NADH) and 5 non-pharmacological therapies (cognitive-behavior-therapy-related treatments, graded-exercise-related therapies, rehabilitation, acupuncture and abdominal tuina). However, there was no definitely effective intervention with coherence and reproducibility. CONCLUSIONS: This systematic review integrates the comprehensive features of previous RCTs for CFS/ME and reflects on their limitations and perspectives in the process of developing new interventions.

Singular value decomposition approach to coherent averaging in digital holography.

We present a new approach to coherent averaging in digital holography using singular value decomposition (SVD). Digital holography enables the extraction of phase information from intensity measurements. For this reason, SVD can be used to statistically determine the orthogonal vectors that align the complex-valued measurements from multiple frames and group common modes accounting for constant phase shift terms. The SVD approach enables the separation of multiple signals, which can be applied to remove undesired artifacts such as scatter in retrieved images. The advantages of the SVD approach are demonstrated here in experiments through fog-degraded holograms with spatially incoherent and coherent scatter.

Ultrafast Shock-Induced Reactions in Pentaerythritol Tetranitrate Thin Films.

The chemical and physical processes involved in the shock-to-detonation transition of energetic solids are not fully understood due to difficulties in probing the fast dynamics involved in initiation. Here, we employ shock interferometry experiments with sub-20-ps time resolution to study highly textured (110) pentaerythritol tetranitrate (PETN) thin films during the early stages of shock compression using ultrafast laser-driven shock wave methods. We observe evidence of rapid exothermic chemical reactions in the PETN thin films for interface particle velocities above ∼1.05 km/s as indicated by shock velocities and pressures well above the unreacted Hugoniot. The time scale of our experiment suggests that exothermic reactions begin less than 50 ps behind the shock front for these high-density PETN thin films. Thermochemical calculations for partially reacted Hugoniots also support this interpretation. The experimentally observed time scale of reactivity could be used to narrow possible initiation mechanisms.

Bandgap Inhomogeneity of a PbSe Quantum Dot Ensemble from Two-Dimensional Spectroscopy and Comparison to Size Inhomogeneity from Electron Microscopy.

Femtosecond two-dimensional Fourier transform spectroscopy is used to determine the static bandgap inhomogeneity of a colloidal quantum dot ensemble. The excited states of quantum dots absorb light, so their absorptive two-dimensional (2D) spectra will typically have positive and negative peaks. It is shown that the absorption bandgap inhomogeneity is robustly determined by the slope of the nodal line separating positive and negative peaks in the 2D spectrum around the bandgap transition; this nodal line slope is independent of excited state parameters not known from the absorption and emission spectra. The absorption bandgap inhomogeneity is compared to a size and shape distribution determined by electron microscopy. The electron microscopy images are analyzed using new 2D histograms that correlate major and minor image projections to reveal elongated nanocrystals, a conclusion supported by grazing incidence small-angle X-ray scattering and high-resolution transmission electron microscopy. The absorption bandgap inhomogeneity quantitatively agrees with the bandgap variations calculated from the size and shape distribution, placing upper bounds on any surface contributions.

Counseling services for Asian, Latino/a, and White American students: Initial severity, session attendance, and outcome.

OBJECTIVE: The current study examined racial/ethnic differences in initial severity, session attendance, and counseling outcomes in a large and diverse sample of Asian American, Latino/a, and White student clients who utilized university counseling services between 2008 and 2012. METHOD: We used archival data of 5,472 clients (62% female; M age = 23.1, SD = 4.3) who self-identified their race/ethnicity as being Asian American (38.9%), Latino/a (14.9%), or White (46.2%). Treatment engagement was measured by the number of counseling sessions attended; initial severity and treatment outcome were measured using the Outcome Questionnaire-45. RESULTS: Asian American clients, particularly Chinese, Filipino/a, Korean, and Vietnamese Americans, had greater initial severity compared with White clients. Asian Indian, Korean, and Vietnamese American clients used significantly fewer sessions of counseling than White clients after controlling for initial severity. All racial/ethnic minority groups continued to have clinically significant distress in certain areas (e.g., social role functioning) at counseling termination. CONCLUSIONS: These findings highlight the need to devote greater attention to the counseling experiences of racial/ethnic minority clients, especially certain Asian American groups. Further research directions are provided. (PsycINFO Database Record

Fluorescence lifetime snapshots reveal two rapidly reversible mechanisms of photoprotection in live cells of Chlamydomonas reinhardtii.

Photosynthetic organisms avoid photodamage to photosystem II (PSII) in variable light conditions via a suite of photoprotective mechanisms called nonphotochemical quenching (NPQ), in which excess absorbed light is dissipated harmlessly. To quantify the contributions of different quenching mechanisms to NPQ, we have devised a technique to measure the changes in chlorophyll fluorescence lifetime as photosynthetic organisms adapt to varying light conditions. We applied this technique to measure the fluorescence lifetimes responsible for the predominant, rapidly reversible component of NPQ, qE, in living cells of Chlamydomonas reinhardtii. Application of high light to dark-adapted cells of C. reinhardtii led to an increase in the amplitudes of 65 ps and 305 ps chlorophyll fluorescence lifetime components that was reversed after the high light was turned off. Removal of the pH gradient across the thylakoid membrane linked the changes in the amplitudes of the two components to qE quenching. The rise times of the amplitudes of the two components were significantly different, suggesting that the changes are due to two different qE mechanisms. We tentatively suggest that the changes in the 65 ps component are due to charge-transfer quenching in the minor light-harvesting complexes and that the changes in the 305 ps component are due to aggregated light-harvesting complex II trimers that have detached from PSII. We anticipate that this technique will be useful for resolving the various mechanisms of NPQ and for quantifying the timescales associated with these mechanisms.

Fluoroquinolone resistant rectal colonization predicts risk of infectious complications after transrectal prostate biopsy.

PURPOSE: Infection after transrectal prostate biopsy has become an increasing concern due to fluoroquinolone resistant bacteria. We determined whether colonization identified by rectal culture can identify men at high risk for post-transrectal prostate biopsy infection. MATERIALS AND METHODS: Six institutions provided retrospective data through a standardized, web based data entry form on patients undergoing transrectal prostate biopsy who had rectal culture performed. The primary outcome was any post-transrectal prostate biopsy infection and the secondary outcome was hospital admission 30 days after transrectal prostate biopsy. We used chi-square and logistic regression statistical analysis. RESULTS: A total of 2,673 men underwent rectal culture before transrectal prostate biopsy from January 1, 2007 to September 12, 2013. The prevalence of fluoroquinolone resistance was 20.5% (549 of 2,673). Fluoroquinolone resistant positive rectal cultures were associated with post-biopsy infection (6.6% vs 1.6%, p <0.001) and hospitalization (4.4% vs 0.9%, p <0.001). Fluoroquinolone resistant positive rectal culture increased the risk of infection (OR 3.98, 95% CI 2.37-6.71, p <0.001) and subsequent hospital admission (OR 4.77, 95% CI 2.50-9.10, p <0.001). If men only received fluoroquinolone prophylaxis, the infection and hospitalization proportion increased to 8.2% (28 of 343) and 6.1% (21 of 343), with OR 4.77 (95% CI 2.50-9.10, p <0.001) and 5.67 (95% CI 3.00-10.90, p <0.001), respectively. The most common fluoroquinolone resistant bacteria isolates were Escherichia coli (83.7%). Limitations include the retrospective study design, nonstandardized culture and interpretation of resistance methods. CONCLUSIONS: Colonization of fluoroquinolone resistant organisms in the rectum identifies men at high risk for infection and subsequent hospitalization from prostate biopsy, especially in those with fluoroquinolone prophylaxis only.

Enhanced interferometric detection in two-dimensional spectroscopy with a Sagnac interferometer.

An intrinsically phase-stable Sagnac interferometer is introduced for optimized interferometric detection in partially collinear two-dimensional (2D) spectroscopy. With a pump-pulse pair from an actively stabilized Mach-Zehnder interferometer, the Sagnac scheme is demonstrated in broadband, short-wave IR (1-2 µm), 2D electronic spectroscopy of IR-26 dye.

circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.

Circular RNAs represent a class of endogenous RNAs that regulate gene expression and influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Using time-course depletion of circHIPK3 and specific candidate RNA-binding proteins, we identify several perturbed genes by RNA sequencing analyses. Expression-coupled motif analyses identify an 11-mer motif within circHIPK3, which also becomes enriched in genes that are downregulated upon circHIPK3 depletion. By mining eCLIP datasets and combined with RNA immunoprecipitation assays, we demonstrate that the 11-mer motif constitutes a strong binding site for IGF2BP2 in bladder cancer cell lines. Our results suggest that circHIPK3 can sequester IGF2BP2 as a competing endogenous RNA (ceRNA), leading to target mRNA stabilization. As an example of a circHIPK3-regulated gene, we focus on the STAT3 mRNA as a specific substrate of IGF2BP2 and validate that manipulation of circHIPK3 regulates IGF2BP2-STAT3 mRNA binding and, thereby, STAT3 mRNA levels. Surprisingly, absolute copy number quantifications demonstrate that IGF2BP2 outnumbers circHIPK3 by orders of magnitude, which is inconsistent with a simple 1:1 ceRNA hypothesis. Instead, we show that circHIPK3 can nucleate multiple copies of IGF2BP2, potentially via phase separation, to produce IGF2BP2 condensates. Our results support a model where a few cellular circHIPK3 molecules can induce IGF2BP2 condensation, thereby regulating key factors for cell proliferation.

circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.

Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Specifically, we use temporal depletion of circHIPK3 or specific RNA binding proteins (RBPs) and identify several perturbed genes by RNA sequencing analyses. Using expression-coupled motif analyses of mRNA expression data from various knockdown experiments, we identify an 11-mer motif within circHIPK3, which is also enriched in genes that become downregulated upon circHIPK3 depletion. By mining eCLIP datasets, we find that the 11-mer motif constitutes a strong binding site for IGF2BP2 and validate this circHIPK3-IGF2BP2 interaction experimentally using RNA-immunoprecipitation and competition assays in bladder cancer cell lines. Our results suggest that circHIPK3 and IGF2BP2 mRNA targets compete for binding. Since the identified 11-mer motif found in circHIPK3 is enriched in upregulated genes following IGF2BP2 knockdown, and since IGF2BP2 depletion conversely globally antagonizes the effect of circHIPK3 knockdown on target genes, our results suggest that circHIPK3 can sequester IGF2BP2 as a competing endogenous RNA (ceRNA), leading to target mRNA stabilization. As an example of a circHIPK3-regulated gene, we focus on the STAT3 mRNA as a specific substrate of IGF2BP2 and validate that manipulation of circHIPK3 regulates IGF2BP2-STAT3 mRNA binding and thereby STAT3 mRNA levels. However, absolute copy number quantifications demonstrate that IGF2BP2 outnumbers circHIPK3 by orders of magnitude, which is inconsistent with a simple 1:1 ceRNA hypothesis. Instead, we show that circHIPK3 can nucleate multiple copies of IGF2BP2, potentially via phase separation, to produce IGF2BP2 condensates. Finally, we show that circHIPK3 expression correlates with overall survival of patients with bladder cancer. Our results are consistent with a model where relatively few cellular circHIPK3 molecules function as inducers of IGF2BP2 condensation thereby regulating STAT3 and other key factors for cell proliferation and potentially cancer progression.

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.

Impact of tumour morphology on renal function decline after partial nephrectomy.

OBJECTIVE: To examine the association of renal morphology with renal function after partial nephrectomy (PN). PATIENTS AND METHODS: We conducted a multi-institutional retrospective analysis of 322 PNs performed between 2003 and 2011. The RENAL nephrometry score for each lesion was determined and the estimated glomerular filtration rate (eGFR) was calculated preoperatively and at last follow-up. We divided patients into two RENAL nephrometry score groups, low (<8) and high (≥8), and analysed and compared the outcomes of each group. The primary outcome was median change in eGFR between preoperative and last follow-up (ΔeGFR). The secondary outcome was eGFR <60 mL/min/1.73 m(2) at last follow-up. Multivariable analysis was conducted to evaluate the risk factors for eGFR <60 mL/min/1.73 m(2) at last follow-up. RESULTS: The median (interquartile range) follow-up was 25.2 (13.5-39.3) months. Low (n = 165) and high (n = 157) RENAL score groups were well-matched for baseline eGFR. The median tumour size (4.2 vs 2.4 cm, P < 0.001) was greater for the high group. In all, 64% of the low and 88.2% of the high RENAL score group (P < 0.001) had decreased eGFR at last follow-up. Median eGFR was -7 for the low vs -13.8 mL/min/1.73 m(2) for the high group (P = 0.001); eGFR <60 mL/min/1.73 m(2) at last follow-up was 27.3% for the low vs 37.6% for the high group (P = 0.057). Linear regression analysis showed that for each 1-point increase in RENAL score, there was 2.5% decrease in eGFR (P = 0.002); for each 1-cm increase in tumour size, there was 1.8% decrease in eGFR (P = 0.013). Area under curve analyses showed no significant difference between RENAL score and tumour size for prediction of de novo eGFR <60 mL/min/1.73 m(2) (P = 0.920) and ΔeGFR ≥50% (P = 0.85). Multivariable analysis showed that increasing RENAL score (odds ratio [OR] 1.24, P = 0.046) and decreasing preoperative eGFR (OR 1.10, P < 0.001) were risk factors for eGFR <60 mL/min/1.73 m(2) at last follow-up. CONCLUSIONS: Increasing RENAL nephrometry score is an independent risk factor for eGFR <60 mL/min/1.73 m(2) after PN. RENAL nephrometry score may serve as an additional measure for risk stratification before PN, but further investigation is required.

A comparison of long term renal functional outcomes following partial nephrectomy and radiofrequency ablation.

INTRODUCTION: To compare long term glomerular filtration rate (GFR) outcomes of partial nephrectomy and radiofrequency ablation performed for renal malignancy. MATERIALS AND METHODS: Renal function of 347 patients undergoing radiofrequency ablation (n = 142) or partial nephrectomy (n = 205) for renal malignancy between 1994 and 2011 were compared from a retrospective database at a single tertiary care center. Minimum 1 year of follow up was required, resulting in a mean follow up of 48.2 (SD +/- 28.2) months. Renal function was estimated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. The primary study outcome was progression of Chronic Kidney Disease (CKD) stage, calculated using the Kaplan-Meier life table method. Multivariate analysis was also conducted to determine the level of association between GFR decline and treatment modality. RESULTS: The 5 year freedom from CKD stage progression for radiofrequency ablation and partial nephrectomy was 85.4% (95% CI 76.8%-91.1%) versus 82.1% (95% CI 73.7%-88.1%) (p = 0.06). A longer follow up interval was associated with greater GFR decline, although hypertension, diabetes, age, and tumor size were not. CONCLUSION: Radiofrequency ablation provides similar long term renal function preservation benefit as partial nephrectomy.

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.