bluuebunny/crossref_metadata_2025 huggingface dataset:
Acquisition of multidrug-resistant Enterobacterales during international travel: a systematic review of clinical and microbiological characteristics and meta-analyses of risk factors
Authors: Voor in ‘t holt Anne F. , Mourik Kees , Beishuizen Berend , van der Schoor Adriënne S. , Verbon Annelies , Vos Margreet C. , Severin Juliëtte A.
Published: May 2020

Background

International tourism increased from 25 million tourist arrivals in 1950 to over 1.3 billion in 2017. These travelers can be exposed to (multi) resistant microorganisms, may become colonized, and bring them back home. This systematic review aims to identify the carriage rates of multidrug-resistant Enterobacterales (MDR-E) among returning travelers, to identify microbiological methods used, and to identify the leading risk factors for acquiring MDR-E during international travel.

Methods

Articles related to our research question were identified through a literature search in multiple databases (until June 18, 2019) - Embase, Medline Ovid, Cochrane, Scopus, Cinahl, Web of Science, and Google Scholar.

Results

Out of 3211 potentially relevant articles, we included 22 studies in the systematic review, and 12 studies in 7 random-effects meta-analyses. Highest carriage rates of MDR-E were observed after travel to Southern Asia (median 71%), followed by travel to Northern Africa (median 42%). Carbapenemase-producing Enterobacterales (CPE) were identified in 5 out of 22 studies, from a few patients. However, in only eight out of 22 studies (36.4%) the initial laboratory method targeted detection of the presence of CPE in the original samples. The risk factor with the highest pooled odds ratio (OR) for MDR-E was travel to Southern Asia (pooled OR = 14.16, 95% confidence interval [CI] = 5.50 to 36.45), followed by antibiotic use during travel (pooled OR = 2.78, 95% CI = 1.76 to 4.39).

Conclusions

Risk of acquiring MDR-E while travelling increases depending on travel destination and if antibiotics are used during travel. This information is useful for the development of guidelines for healthcare facilities with low MDR-E prevalence rates to prevent admission of carriers without appropriate measures. The impact of such guidelines should be assessed.
Use of social network analysis to examine preferential co-occurrences in Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus Mitchill, 1815
Authors: Lilly Jessie , McLean Montana F. , Dadswell Michael J. , Wirgin Isaac , Comolli Perry , Stokesbury Michael J. W.
Published: May 2020

Background

Application of Social Network Analysis (SNA) to acoustic telemetry is a useful approach to examine social behavior in fish. Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus) are ancient, long-lived anadromous finfish. Although Atlantic Sturgeon have been the subject of numerous telemetry studies, none have used SNA to analyze their co-occurrence behavior. During 2010–2014 Atlantic Sturgeon (n = 103) that were later genetically identified as being from the Saint John River, Canada and the Kennebec River, US were captured by otter trawl and brush weir in Minas Basin, Bay of Fundy, Canada, and acoustically tagged. Using data from moored acoustic receivers within foraging habitat in Minas Basin, we tested if Atlantic Sturgeon formed social associations that were random or structured during 2012 to 2014; and whether these co-occurrences consisted of individuals from the same river of origin or capture date.

Results

Irrespective of genetic origin and initial capture date, Atlantic Sturgeon formed co-occurrences in Minas Basin that were significantly different than would be observed by chance during 2012 and very close to significant during 2013. Analysis demonstrated that some Atlantic Sturgeon preferentially co-occur within their primary feeding habitat.

Conclusions

The current threats to Atlantic Sturgeon aggregations within the Bay of Fundy, Nova Scotia, include bycatch in fisheries throughout their coastal migration routes and more recently the development of tidal turbines along their migratory corridor to their summer aggregation site. It is important to determine if Atlantic Sturgeon form aggregations with conspecifics from the same population to inform management decisions regarding threats to groups of individuals. This study indicated that Atlantic Sturgeon may form preferential co-occurrences within their feeding aggregation and co-occurrences that were identified were not dependent upon population of origin or initial capture date.
Measuring university students’ interest in biology: evaluation of an instrument targeting Hidi and Renninger’s individual interest
Authors: Knekta Eva , Rowland Ashley A. , Corwin Lisa A. , Eddy Sarah
Published: May 2020

Background

Boosting students’ disciplinary interest has long been considered an important mechanism to increase student success and retention in STEM education. Yet, interest is a complex construct and can mean different things to different people, and many of the existing interest questionnaires do not identify a specific theoretical framework underlying their items. To demonstrate that curricular interventions targeting students’ interest are effective, educators need a theoretically based instrument to measure interest. The aim of this study was to develop an instrument measuring undergraduate students’ interest in the discipline of biology and collect initial validity evidence supporting the proposed use. The instrument structure is based on Hidi and Renninger’s (Educational Psychologist 41:111–127, 2006) conceptualization of individual interest, and the intended use is to evaluate changes in the biology interests of the US undergraduate students pursuing STEM degrees. To provide evidence of validity, the instrument was completed by 446 biology majors and 489 non-biology majors at two R1 universities. Exploratory and confirmatory factor analyses were applied to evaluate the internal structure of the instrument.

Results

The final three-factor instrument supported by these analyses includes 6 items representing positive feelings towards biology, 5 items representing personal value of biology, and 8 items representing reengagement in biology-related activities. Measurement invariance across biology and non-biology majors was established and subsequent comparisons of these populations demonstrated that biology majors report significantly higher positive feelings, personal value, and reengagement in biology-related activities compared to non-biology majors.

Conclusions

The study findings support the use of the instrument to gain a broad understanding of students’ individual interest in biology. With minor adaptions, the instrument could also be evaluated for use in other STEM disciplines and for use by other populations.
Landslide susceptibility evaluation and hazard zonation techniques – a review
Authors: Shano Leulalem , Raghuvanshi Tarun Kumar , Meten Matebie
Published: May 2020

Landslides are the most destructive geological hazard in the hilly regions. For systematic landslide mitigation and management, landslide evaluation and hazard zonation is required. Over the past few decades several techniques have been developed that can be used for landslide evaluation and zonation. These techniques can broadly be classified into qualitative and quantitative approaches. Qualitative approaches include geomorphological analysis and heuristic techniques whereas quantitative approaches include statistical, artificial intelligence and deterministic techniques. In quantitative techniques prediction for landslide susceptibility is based on the actual realistic data and interpretations. Further, the quantitative techniques also overcome the subjectivity of qualitative approaches. Each of these techniques may consider different causative factors and utilizes various means for factor evaluation and analysis. When compared, each of these techniques has its own advantage and disadvantage over other techniques. The selection of appropriate technique for landslide hazard evaluation and zonation is very crucial. The factors that need to be considered to adopt an appropriate approach are; investigation purpose, the extent of the area to be covered, the type of mapping units, the scale of map to be produced, type of data to be used, type of landslides, availability of resources, capability and skill set of an evaluator and the accessibility to the study area. The main aim of this article is to present a comprehensive review on various techniques and approaches available for landslide susceptibility and hazard zonation mapping. Further, attempt is also made to assess the effectiveness of these techniques in landslide hazard zonation studies.
When it all falls down: the relationship between intuitive physics and spatial cognition
Authors: Mitko Alex , Fischer Jason
Published: May 2020

Our intuitive understanding of physical dynamics is crucial in daily life. When we fill a coffee cup, stack items in a refrigerator, or navigate around a slippery patch of ice, we draw on our intuitions about how physical interactions will unfold. What mental machinery underlies our ability to form such inferences? Numerous aspects of cognition must contribute - for example, spatial thinking, temporal prediction, and working memory, to name a few. Is intuitive physics merely the sum of its parts - a collection of these and other related abilities that we apply to physical scenarios as we would to other tasks? Or does physical reasoning rest on something extra - a devoted set of mental resources that takes information from other cognitive systems as inputs? Here, we take a key step in addressing this question by relating individual differences on a physical prediction task to performance on spatial tasks, which may be most likely to account for intuitive physics abilities given the fundamentally spatial nature of physical interactions. To what degree can physical prediction performance be disentangled from spatial thinking? We tested 100 online participants in an “Unstable Towers” task and measures of spatial cognition and working memory. We found a positive relationship between intuitive physics and spatial skills, but there were substantial, reliable individual differences in physical prediction ability that could not be accounted for by spatial measures or working memory. Our findings point toward the separability of intuitive physics from spatial cognition.
Mono and binuclear cobalt(II) mixed ligand complexes containing 1,10-phenanthroline and adenine using 1,3-diaminopropane as a spacer: synthesis, characterization, and antibacterial activity investigations
Authors: Abebe Atakilt , Bayeh Yosef , Belay Minale , Gebretsadik Tesfay , Thomas Madhu , Linert Wolfgang
Published: May 2020

Background

Coordination compounds, in particular cobalt(II) mixed ligand complexes containing 1,10-phenantroline, have drawn the attention of many investigators as some of them are showing antimicrobial activities.

Result

Herein, we report three novel mixed ligand complexes of cobalt(II) having the formulae [Co(L1)2(H2O)2]Cl2, [Co(L1)2(L2)(H2O)]Cl2 and [Co2(L1)4(L2)2(L3)]Cl4 (L1 = 1,10-phenanthroline, L2 = adenine, L3 = 1,3-diaminepropane) were synthesized and characterized by elemental analysis, conductivity measurement, infrared, and UV-Vis spectroscopic techniques. Octahedral geometries are proposed to all the complexes. In vitro antibacterial activities of the ligands, salt, and metal complexes were tested on four pathogenic bacteria (Staphylococcus aureus, Salmonella typhus, Escherichia coli, and Staphylococcus epidermis) using disc diffusion method.

Conclusions

It is interesting to note that the newly synthesized cobalt(II) complexes are active against gram negative bacteria (Escherichia coli and Klebsiella pneumoniae) even though cobalt(II) complexes are well known for their activity against gram positive bacteria.
Improving the crosscorrelation method to estimate the total magnetization direction vector of isolated sources: A space-domain approach for unstable inclination values
Authors: Ribeiro-Filho Nelson , Bijani Rodrigo , Ponte-Neto Cosme
Published: May 2020

Knowledge of the total magnetization direction of geologic sources is valuable for interpretation of magnetic anomalies. Although the magnetization direction of causative sources is assumed to be induced by the ambient magnetic field, the presence of remanence should not be neglected. An existing method of correlating total and vertical gradients of the reduced-to-the-pole (RTP) anomaly estimates the total magnetization direction well. However, due to the numerical instability of RTP transformation in the Fourier domain, an assumption should be considered for dealing with inclination values at approximately 0°. We have adopted an extension to the standard crosscorrelation method for estimating the total magnetization direction vector, computing the RTP anomaly by means of the classic equivalent layer technique for low inclination values. Additionally, an ideal number of equivalent sources within the layer is considered for reducing the computational demands. To investigate the relevant aspects of the adopted method, two simple synthetic scenarios are presented. First, a magnetic anomaly produced by a homogeneous and isolated vertical dike is considered. This test illustrates the good performance of the adopted approach, finding the true magnetization direction, even for low inclination values. In the second synthetic test, a long-wavelength component is added to the previous magnetic total-field anomaly. In this case, the method adopted here fails to estimate a reliable magnetization direction vector, showing weak performance for strong interfering magnetic anomalies. On the real data example, the application tests an isolated total-field anomaly of the Carajás Mineral Province, in northern Brazil, where the inclination of the ambient magnetic field is close to zero. The obtained results indicate weak remanence in the estimated total magnetization direction vector, which would never be reached in the standard formulation of the crosscorrelation technique.
Association of prior depressive symptoms and suicide attempts with subsequent victimization: analysis of population-based data from the Adult Psychiatric Morbidity Survey
Authors: Bhavsar Vishal , Hatch Stephani L , Dean Kimberlie , McManus Sally
Published: May 2020

Background:

Symptoms of mental disorder, particularly schizophrenia, predispose to victimization. Much less is known about the relationship between depressive symptoms and later victimization in the general population, the influence of these symptoms on types of subsequent victimization, or the role of symptom severity. We investigated this in nationally representative data from the United Kingdom.

Methods:

Data were from the Adult Psychiatric Morbidity Survey 2007. Multivariable logistic regressions estimated association between (a) prior depressive symptoms, (b) prior depressive symptoms with suicide attempt, and types of more recent victimization. Gender-specific associations were estimated using multiplicative interactions.

Results:

Prior depressive symptoms were associated with greater odds of any recent intimate partner violence (IPV), emotional IPV, sexual victimization, workplace victimization, any victimization, and cumulative victimization (adjusted odds ratio [aOR] for increasing types of recent victimization: 1.47, 95% confidence interval [CI]: 1.14, 1.89). Prior depressive symptoms with suicide attempt were associated with any recent IPV, emotional IPV, any victimization, and cumulative victimization (aOR for increasing types of recent victimization: 2.33, 95% CI: 1.22, 4.44). Self reported recalled data on previous depressive symptoms may have limited accuracy. Small numbers of outcomes for some comparisons results in imprecision of these estimates.

Conclusions:

Aside from severe mental illness such as schizophrenia, previous depressive symptoms in the general population are associated with greater subsequent victimization. Men and women with prior depressive symptoms may be vulnerable to a range of types of victimization, and may benefit from interventions to reduce this vulnerability.
Provider Recommendations for Phase I Clinical Trials Within a Shared Decision-Making Model in Phase I Cancer Clinical Trial Discussions
Authors: Hianik Rachel S. , Campbell Gavin P. , Abernethy Eli , Lewis Colleen , Wu Christina S. , Akce Mehmet , Dixon Margie D. , Shaib Walid L. , Pentz Rebecca D.
Published: May 2020

PURPOSE:

Debate continues over whether explicit recommendations for a clinical trial should be included as an element of shared decision making within oncology. We aimed to determine if and how providers make explicit recommendations in the setting of phase I cancer clinical trials.

METHODS:

Twenty-three patient/provider conversations about phase I trials were analyzed to determine how recommendations are made and how the conversations align with a shared decision-making framework. In addition, 19 providers (9 of whose patient encounters were observed) were interviewed about the factors they consider when deciding whether to recommend a phase I trial.

RESULTS:

We found that providers are comprehensive in the factors they consider when recommending clinical trials. The two most frequently stated factors were performance status (89%) and patient preferences (84%). Providers made explicit recommendations in 19 conversations (83%), with 12 of those being for a phase I trial (12 [63%] of 19). They made these recommendations in a manner consistent with a shared decision-making model; 18 (95%) of the 19 conversations during which a recommendation was made included all steps, or all but 1 step, of shared decision making, as did 11 of the 12 conversations during which a phase I trial was recommended. In 7 (58%) of these later conversations, providers also emphasized the importance of the patient’s opinion.

CONCLUSION:

We suggest that providers not hesitate to make explicit recommendations for phase I clinical trials, because they are able to do so in a manner consistent with shared decision making. With further research, these results can be applied to other clinical trial settings.
Foundation One Genomic Interrogation of Thyroid Cancers in Patients With Metastatic Disease Requiring Systemic Therapy
Authors: Iñiguez-Ariza Nicole M , Jasim Sina , Ryder Mabel M , Chintakuntlawar Ashish V , Morris John C , Hilger Crystal R , Menefee Michael E , Smallridge Robert C , Karlin Nina J , Alcaino Constanza , Bible Keith C
Published: May 2020

Context

Clinical applications of genomic assessment of thyroid cancers are rapidly evolving.

Objectives, Design, and Setting

We studied tumor samples from patients with imminently threatening and rare thyroid cancers to identify genomic alterations that might correlate with outcomes and/or be productively therapeutically targetable.

Patient Context

Progressive and metastatic, and/or rare, thyroid cancers were studied, 2012 to 2016, at Mayo Clinic sites.

Intervention

The intervention was Foundation One tumor interrogation.

Main Outcome Measures

Main outcome measures included genomic alterations, patient characteristics, and overall survival.

Results

Samples from 55 patients were evaluated: 20 anaplastic thyroid cancers (ATCs) (36%), 25 radioactive iodine–refractory differentiated thyroid cancers (DTCs)/poorly differentiated thyroid cancers (PDTCs) (45%; 14 papillary thyroid cancer [PTCs], 6 PDTCs, 5 Hürthle cell cancers), 8 medullary thyroid cancers (MTCs) (15%), and 2 others (a spindle epithelial tumor with thymus-like differentiation, and a primary thyroid sarcoma). Overall, 72% of DTCs, 79% of ATCs, and 75% of MTCs were deemed to have potentially productively targetable alterations. The most commonly encountered mutation was of TERT promoter (56% of DTCs, 68% of ATCs)—but this is not presently targetable. Targetable BRAFV600E mutations were found in 40% of DTCs/PDTCs (83% of PTCs) and 32% of ATCs; of MTCs, 75% had targetable RET mutations, and 25% HRAS mutations. Of patient tumors with nonmutated BRAFV600E, 53% of DTC/PDTCs and 69% of ATCs had other potentially productively targetable mutations. Genomic alterations in our series of poor prognosis metastatic DTC/PDTCs also closely resembled those seen in ATC.

Conclusions

Whereas genomic interrogation of favorable prognosis thyroid cancer seems ill advised, potentially productively targetable mutations were demonstrated in the majority of tumors from patients with metastatic thyroid cancers requiring systemic therapy, suggesting a rationale for the selective application of this technology.
Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA
Authors: Brillet Karl , Martinez-Zapien Denise , Bec Guillaume , Ennifar Eric , Dock-Bregeon Anne-Catherine , Lebars Isabelle
Published: May 2020

The 7SK small nuclear RNA (7SKsnRNA) plays a key role in the regulation of RNA polymerase II by sequestrating and inhibiting the positive transcription elongation factor b (P-TEFb) in the 7SK ribonucleoprotein complex (7SKsnRNP), a process mediated by interaction with the protein HEXIM. P-TEFb is also an essential cellular factor recruited by the viral protein Tat to ensure the replication of the viral RNA in the infection cycle of the human immunodeficiency virus (HIV-1). Tat promotes the release of P-TEFb from the 7SKsnRNP and subsequent activation of transcription, by displacing HEXIM from the 5'-hairpin of the 7SKsnRNA. This hairpin (HP1), comprising the signature sequence of the 7SKsnRNA, has been the subject of three independent structural studies aimed at identifying the structural features that could drive the recognition by the two proteins, both depending on arginine-rich motifs (ARM). Interestingly, four distinct structures were determined. In an attempt to provide a comprehensive view of the structure-function relationship of this versatile RNA, we present here a structural analysis of the models, highlighting how HP1 is able to adopt distinct conformations with significant impact on the compactness of the molecule. Since these models are solved under different conditions by nuclear magnetic resonance (NMR) and crystallography, the impact of the buffer composition on the conformational variation was investigated by complementary biophysical approaches. Finally, using isothermal titration calorimetry, we determined the thermodynamic signatures of the Tat-ARM and HEXIM-ARM peptide interactions with the RNA, showing that they are associated with distinct binding mechanisms.
Inventory Sharing and Demand-Side Underweighting
Authors: Zhao Hui , Xu Liang , Siemsen Enno
Published: May 2020

Problem definition : Transshipment/inventory sharing has been used in practice because of its risk-pooling potential. However, human decision makers play a critical role in making inventory decisions in an inventory sharing system, which may affect its benefits. We investigate whether the opportunity to transship inventory influences decision makers’ inventory decisions and whether, as a result, the intended risk-pooling benefits materialize. Academic/practical relevance : Previous research in transshipment, which is focused on finding optimal stocking and sharing decisions, assumes rational decision making without any systematic bias. As one of the first to study inventory sharing from a behavioral perspective, we demonstrate a persistent stocking-decision bias relevant for inventory sharing systems. Methodology : We develop a behavioral model of a multilocation inventory system with transshipments. Using four behavioral studies, we identify, test, estimate, and mitigate a demand-side underweighting bias: although inventory sharing brings both a supply-side benefit and a demand-side benefit, players underestimate the latter. We show analytically that such bias leads to underordering. We also explore whether reframing the inventory sharing decision reduces this bias. Results : Our results show that subjects persistently reduce their order quantities when transshipments are allowed. This underordering, which persists even when a decision-support system suggests optimal quantities, causes insufficient inventory in the system, in turn reducing the risk-pooling benefits of inventory sharing. Underordering is evidently caused by an underweighting bias; although players correctly estimate the supply-side potential from transshipment, they only estimate 20% of the demand-side potential. Managerial implications : Although inventory sharing can profitably reduce inventory, too much underordering undermines its intended risk-pooling benefits. The demand-side benefits of transshipment need to be emphasized when implementing inventory sharing systems.
Managing trauma and orthopaedic outpatient services during the COVID-19 pandemic: early experience
Authors: Iyengar Karthikeyan , Sangani Chetan , Adam Riad F
Published: May 2020

As the COVID-19 pandemic took hold in the UK, the effects on the NHS, its resources and clinical services have been profound. This article describes the authors' early experience in managing outpatient services in the trauma and orthopaedics department to provide continuity of care to patients.
Community event sustainability: why don’t people volunteer?
Authors: Hallett R.J. , Mullan N.K. , Tideswell A.E. , Haake S.J. , Graney M. , Hurley M.V.
Published: May 2020

Every Saturday, thousands of runners worldwide participate in parkrun – a free five-kilometre run/walk event. Delivery relies on volunteers, and parkrunners are encouraged to volunteer regularly. However, volunteer recruitment is often difficult, and this study aimed to investigate the underpinning reasons for this. Data were collected from 6,749 parkrunners using an online survey, including 860 who had never volunteered. In addition to demographic information and views on incentives, non-volunteers were asked to rate agreement level for 18 statements about not volunteering. Main reasons were preferring to run or walk and not having got round to it. Principal component analysis indicated four underlying factors: inertia, self-interest, lack of knowledge and anxiety. Non-volunteers were younger, slower runners and walkers, less frequent parkrun attendees and had become involved more recently than volunteers. Ease of signing up to volunteer and being unsure of the commitment required were barriers. It is recommended that these two issues are addressed to help volunteer recruitment.
Governmental social work (part 1): the tyranny of transformation
Authors: Harris John , Shergill Makhan
Published: May 2020

Governmental social work refers to a new ‘settlement’ for social work and social work education. A critical discourse analysis of Putting children first (Department for Education, 2016) – considered the foundational text of governmental social work – is undertaken. The analysis suggests the ways in which the transformative strategy of governmental social work seeks to achieve outcomes or objectives within existing structures and practices, especially by changing them in particular ways. Social workers are called on to become free progressive professionals as long as they comply with the form of professionalism that is legitimated by governmental social work. The reforms are represented as the only morally and professionally right responses for those who care about children. This involves a double shuffle: a process of de-professionalisation and re-professionalisation that involves identity change and subjugation for social workers in a compliant profession that increasingly ‘governs itself’ in the required ways and maintains a silence on the circumstances of children’s lives.
Dynamically tunable reflecting near-infrared bandpass filter based on a hybrid graphene–nanometallic structure
Authors: Mirnia Seyed Edriss , Lail Brian A.
Published: May 2020

A dynamically tunable reflecting near-infrared bandpass filter based on a hybrid graphene–nanometallic structure is demonstrated by numerical simulation. The proposed filter is constructed by unit cells with a graphene monolayer embedded into the nanometallic grating structure. The gradual transition of the graphene monolayer from a very thin metal to dielectric plays the key role in tuning the reflection spectrum of the structure. Spectral analysis clearly shows a passband blueshift with increasing graphene Fermi energy. The filter parameters are investigated by varying graphene Fermi energy through external voltage gates. The modulation depth, center frequency, bandwidth, and quality factor of the filter could be tuned. We achieved stable modulation depth as high as 0.735, and a quality factor as high as 3.4. The center frequency can be tuned in a broad range from 210 to 230 THz and with bandwidth tuning from 60 to 95 THz. The effect of the nanogap size and environment refractive index is also numerically investigated. These results are very promising for future use and integration of the proposed filters as a key element of optical communication systems and infrared sensing.
Polarizing interferometer for the unambiguous determination of the ellipsometric parameters
Authors: Röseler Arnulf , Schade Ulrich
Published: May 2020

We report on a polarizing interferometer-ellipsometer arrangement that overcomes the need for additional measurements with a retarder for the unambiguous determination of the ellipsometric parameters in the far infrared spectral range. It consists of a Martin–Puplett interferometer and a wire-grid polarizer as an analyzer. The application of such interferometer-ellipsometer is experimentally demonstrated on a polyethylene sample deriving the refractive index and the thickness in the spectral range between 15 and

35

c
m

−
1

. Based on these results, a similar solution without a retarder for the mid-infrared spectral region is additionally proposed.
Fast TIRF-SIM imaging of dynamic, low-fluorescent biological samples
Authors: Roth Julian , Mehl Johanna , Rohrbach Alexander
Published: May 2020

Fluorescence microscopy is the standard imaging technique to investigate the structures and dynamics of living cells. However, increasing the spatial resolution comes at the cost of temporal resolution and vice versa. In addition, the number of images that can be taken in sufficiently high quality is limited by fluorescence bleaching. Hence, super-resolved imaging at several Hertz of low fluorescent biological samples is still a big challenge and, especially in structured illumination microscopy (SIM), is often visible as imaging artifacts. In this paper, we present a TIRF-SIM system based on scan-mirrors and a Michelson interferometer, which generates images at 110 nm spatial resolution and up to 8 Hz temporal resolution. High resolution becomes possible by optimizing the illumination interference contrast, even for low fluorescent, moving samples. We provide a framework and guidelines on how the modulation contrast, which depends on laser coherence, polarization, beam displacement or sample movements, can be mapped over the entire field of view. In addition, we characterize the influence of the signal-to-noise ratio and the Wiener filtering on the quality of reconstructed SIM images, both in real and frequency space. Our results are supported by theoretical descriptions containing the parameters leading to image artifacts. This study aims to help microscopists to better understand and adjust optical parameters for structured illumination, thereby leading to more trustworthy measurements and analyses of biological dynamics.
Standardising an infant fNIRS analysis pipeline to investigate neurodevelopment in global health
Authors: Bulgarelli Chiara , Blasi Anna , Pollonini Luca , Lloyd-Fox Sarah , Pirazzoli Laura , Perdue Katherine L. , Nelson Charles A. , Elwell Clare E.
Published: May 2020

Data analysis methods for infant fNIRS data in global health are not standardised yet. This work proposes an analysis pipeline that improves the quality of the recovered HRF for use by other researchers in this field.
Overcoming the Fundamental Limit of Two-Photon Microscopy With Non-Degenerate Excitation
Authors: Sadegh Sanaz , Yang Mu-Han , Cheng Xiaojun , Thunemann Martin , Saisan Payam A. , Boas David A. , Fainman Yeshaiahu , Devor Anna
Published: May 2020

We use non-degenerate two-photon excitation where the two excitation beams are displaced in space outside the focal volume to increase the signal-to-background ratio (SBR), overcoming the fundamental penetration depth limit of conventional two-photon microscopy.
Wide-field optical imaging along the neurovascular coupling pathway
Authors: Wang Xiaodan , Bice Annie R. , Bauer Adam Q.
Published: May 2020

We developed a dual fluorophore imaging system for simultaneous, high-speed mapping of neural, metabolic, and hemodynamic activity. Proof-of-concept measurements of spontaneous and stimulus-evoked dynamics are presented in awake and anesthetized mice.
Light splitting and stopping and their combination via controllable Bloch oscillation in a lattice
Authors: Du Lei , Zhang Yan
Published: May 2020

We study controllable Bloch oscillation and its potential applications in a one-dimensional lattice with partly phase-modulated hopping rates. Under proper conditions, such a system can be built by using a quasi-one-dimensional sawtooth lattice with Peierls phases induced by a synthetic magnetic field. The amplitude of the Bloch oscillation can be adjusted precisely and continuously by adjusting the phase, and hence we realize tunable light splitting in the presence of a V-type potential. Moreover, we construct two distinct sandwich structures to realize tunable light stopping and delayed splitting, respectively, of which the stopping and delay durations are tunable. Our proposal may imply exciting opportunities for potential applications in optical communications and photonic device fabrication involving unconventional light transports.
Evaluation of Silicon Photomultiplier Technology for Laser Scanning Microscopy
Authors: Giacomelli Michael G.
Published: May 2020

Photomultiplier tubes are the standard for high sensitivity detection of fluorescence signals, but are costly, fragile, have limited QE and worse sensitivity at far-red wavelengths. Silicon photomultipliers (SIPMs) combine the higher shot-noise limited sensitivity of silicon sensors with the single photon sensitivity of PMTs and can provide higher SNR over a range of common confocal and multiphoton applications. We show how to design low cost electronics that enable extremely high sensitivity, dynamic range, and bandwidth and discuss how to customize high sensitivity detectors for high speed fluorescent imaging.
Light-sheet micro-dissection microscopy for improved molecular analysis of clinical specimens
Authors: Glaser Adam K. , Reder Nicholas P. , Liu Jonathan T.C.
Published: May 2020

In recent years we have developed open-top light-sheet microscopes for a variety of clinical applications. Here we present a new light-sheet micro-dissection microscope for improved molecular analysis of intact tissue specimens.
Image refocusing of miniature CMOS image sensor with angle-selective pixels
Authors: Sugie Kenji , Sasagawa Kiyotaka , Guinto Mark Christian , Haruta Makito , Tokuda Takashi , Ohta Jun
Published: May 2020

We propose an ultra-compact lensless CMOS image sensor that comprises angle-selective pixels and normal pixels. We have demonstrated that the image resolution can be recovered from blurred images by combining this sensor with image processing.
Spatial Resolution Improvement of Lensless Fluorescence Imaging Device with Hybrid Emission Filter
Authors: Sasagawa Kiyotaka , Sugie Kenji , Ohta Yasumi , Kawahara Mamiko , Takehara Hironari , Haruta Makito , Ohta Jun
Published: May 2020

In this study, we fabricated a miniaturized fluorescence imaging system using a laser spot array and a lensless imaging device with hybrid filter. Based on the scanning technique, the spatial resolution was improved.
A novel denoising reconstruction algorithm for multi-height lensless microscopy
Authors: Zhou You , Hua Xia , Song Weizhi , Cao Xun
Published: May 2020

We introduce the Wirtinger gradient descent optimization into the multi-height lensless microscopy for noise-robust and high-quality reconstruction.
Robust Quantitative Phase Imaging Cytometry with Transfer Learning
Authors: Lo Michelle C.K. , Stassen Shobana V. , Siu Dickson M.D. , Tsia Kevin K.
Published: May 2020

We present high-throughput quantitative phase imaging cytometry (>10,000 cells/sec) assisted by neural-networked-based transfer learning that critically overcomes the batch effects and enables accurate label-free multi-class lung cancer types classification at single-cell precision (>91%).
Deep learning-enabled computational cytometer using magnetically-modulated coherent imaging
Authors: Liu Tairan , Zhang Yibo , Ouyang Mengxing , Ray Aniruddha , Kong Janay , Bai Bijie , Kim Donghyuk , Guziak Alexander , Luo Yi , Feizi Alborz , Tsai Katherine , Duan Zhuoran , Liu Xuewei , Kim Danny , Cheung Chloe , Yalcin Sener , Koydemir Hatice Ceylan , Garner Omai B. , Di Carlo Dino , Ozcan Aydogan
Published: May 2020

We present a cost-effective and high-throughput computational cytometer using a magnetically-modulated lensless imaging technique and deep learning-based classification, to rapidly detect rare cells in whole blood, achieving a detection limit of 10 cells/mL.
Advances in fast multiphoton microscopy using light-sheet illumination
Authors: Malkinson Guy , Maioli Vincent , Boniface Antoine , Mahou Pierre , Ortas Júlia Ferrer , Abdeladim Lamiae , Chaudan Élodie , Sonay Ali Y. , Gacoin Thierry , Pantazis Periklis , Beaurepaire Emmanuel , Supatto Willy
Published: May 2020

We report on recent advances in multiphoton light-sheet microscopy to perform fast multimodal imaging combining fluorescence with second-harmonic generation and to mitigate photodamage during in vivo imaging of embryos.
Label-Free Live-Cell Imaging with Interferometric Scattering Microscopy: Confocal Imaging and High-Speed 3D Single Particle Tracking
Authors: Küppers Michelle , Kashkanova Anna , Lühr Jennifer , Albrecht David , Schambony Alexandra , Sandoghdar Vahid
Published: May 2020

The combination of interferometric scattering microscopy (iSCAT) in wide-field and confocal detection reveals new prospects for the label-free visualization of subcellular processes and tracking of nanoscopic matter such as viruses, vesicles and lipid droplets.
3D Single Molecule Localization Microscopy via Deep Learning
Authors: Li Xiaoxu , Yang Runzhao , Guo Yuchen , Qiao Hui , Dai Qionghai
Published: May 2020

We propose a deep-learning based approach to estimate 3D locations of multiple emitters over a large axial range with high accuracy. Localization performance is validated by several experiments on public benchmarks.
Fast Label-free Photoacoustic Microscopy
Authors: Baik Jin Woo , Kim Hyojin , Kim Jongbeom , Kim Jin Young , Son Myeongjoo , Byun Kyunghee , Choi Haeyoung , Ryu Seon Young , Kim Chulhong
Published: May 2020

Photoacoustic microscopy (PAM) is an emerging hybrid imaging modality which maps superior optical contrast acoustically through the photoacoustic effect. Compared with pure optical microscopic imaging modalities, PAM employs absorption contrast rather than scattering contrast, which showed capability for exploring anatomical, functional, and molecular information in biological tissues without exogenous agents. Here, we present fast label-free photoacoustic microscopy, successfully reconstructing the microvasculature in a mouse ear and histopathological features in a mouse uterus.
In-vivo, non-contact, cellular resolution imaging of the human cornea and limbus with a line-scan OCT
Authors: Bizheva Kostadinka , Han Le , Hosseinaee Zohreh , Chen Lin Kun
Published: May 2020

A line-scan, spectral-domain optical coherence tomography system with ~2 µm axial and ~4.5 lateral resolution and line rate of 2,500 B-scans/s was built for in-vivo, non-contact, cellular resolution imaging of the human cornea and limbus.
Terahertz birefringence anisotropy and relaxation effects in polymer-dispersed liquid crystal doped with gold nanoparticles
Authors: Ji Yun-Yun , Fan Fei , Zhang Xin , Cheng Jie-Rong , Chang Sheng-Jiang
Published: May 2020

Terahertz (THz) birefringence anisotropy of the polymer-dispersed liquid crystal (PDLC) doped with gold nanoparticles (Au NPs) is investigated by using terahertz time domain polarization spectroscopy. Controlled by the electric field, the change rate of refractive index for PDLC doped with Au NPs is 0.91% V−1 as the voltage increases, smaller than the pure PDLC, which indicates that the response of the PDLC doped with Au NPs to electric field is more uniform than that of pure PDLC. Therefore, the PDLC doped with Au NPs is more suitable for tunable phase shifters. Furthermore, we found that under the high-frequency alternating electric field, the anisotropic polarization effect of PDLC will disappear to this electric field, namely polarization relaxation phenomenon. However, the results show that the PDLC doped with Au NPs can respond to an electric field with higher alternating frequencies, and the relaxation frequency of PDLC with an Au NPs concentration of 0.2 wt% was improved over two times compared with the pure PDLC and four times higher than that of the precursor mixture without ultraviolet radiation. This work has the significance for the potential applications of tunable THz liquid crystal phase and polarization devices, providing a more uniform and faster relaxation response to the operating electric field.
Modified ray transfer matrix method for accurate non-sequential ray tracing between arbitrary reflective mirrors
Authors: Cao Biao , Yang Huajun , Jiang Ping , Caiyang Weinan , Zhou Miaofang , Mao Shengqian , Qin Yan
Published: May 2020

The ray transfer matrix method is widely used for analyzing beam-transmission properties and designing multi-pass systems. In this paper, a modified ray transfer matrix method is proposed for tracing an accurate non-sequential ray in three-dimensional space based on a vector reflection theory. The modified ray transfer matrix method can be utilized to analyze a ray transmitting between arbitrary surfaces, which is not confined to rotational symmetrical structures. There is no need to project rays onto two perpendicular planes, nor to introduce a paraxial approximation in our calculation. Since the length and angle of every ray can be calculated accurately, almost no deviation is accumulated in multi-pass system. The modified ray transfer matrix method can be applied in optical design, especially in the design of multi-pass cavities and multi-pass cells.
A single-passband microwave photonic filter with kHz bandwidth
Authors: Wen Huashun , Zhu Ning Hua
Published: May 2020

A single-passband microwave photonic filter with 3 dB bandwidth of 12 ± 2.5 kHz over spectral range of 2-40 GHz is experimentally demonstrated by optical-injection of a single-frequency Brillouin fiber laser.
Widefield fluorescence localization microscopy for transcranial imaging of cortical perfusion with capillary resolution
Authors: Chen Zhenyue , Zhou Quanyu , Robin Justine , Razansky Daniel
Published: May 2020

Imaging of cerebral vasculature is impeded with the existing fluorescence microscopy methods due to intense light scattering in living tissues and the need for highly invasive craniotomy procedures to resolve structures on a capillary scale. We propose a widefield fluorescence localization microscopy technique for high-resolution transcranial imaging and quantitative assessment of cortical perfusion in mice. The method is based on tracking single fluorescent microparticles sparsely distributed in the blood stream using a simple CMOS camera and a continuous-wave laser source. We demonstrate quantitative transcranial in vivo mapping of the blood flow velocity and direction at capillary level resolution (5 µm) across the entire cortex. The new technique opens a new high-resolution transcranial window into the brain function in health and disease.
All-fiber Mamyshev oscillator enabled by chirped fiber Bragg gratings
Authors: Boulanger Vincent , Olivier Michel , Guilbert-Savary Félix , Trépanier François , Bernier Martin , Piché Michel
Published: May 2020

We present a linear cavity self-polarizing Mamyshev oscillator at 1550 nm made fully of polarization-maintaining fibers. The cavity filters are chirped fiber Bragg gratings with a Gaussian reflectivity profile that allow for greater reflectivity, larger bandwidth, and dispersion control. This mode-locked fiber laser architecture shows an unprecedented simplicity while delivering 21.3-nJ pulses compressed to 108 fs with a competitive 22.3% pump conversion efficiency. Mode locking is initiated with an external saturable absorber mirror. Numerical simulations show how nonlinearity can be managed with highly dispersive filters inside a Mamyshev oscillator.
Fast sensitive diffuse correlation spectroscopy with a SPAD array
Authors: Liu Wenhui , Qian Ruobing , Xu Shiqi , Konda Pavan Chandra , Horstmeyer Roarke
Published: May 2020

We develop a highly parallelized DCS system using a 32×32 single-photon avalanche diode array, and demonstrate its sensitivity improvement in a DMD-based phantom study and anin vivoforehead blood flow experiment.
Beyond diffuse correlations: deciphering random flow in time-of-flight resolved light dynamics
Authors: Du Le V. N. , Kholiqov Oybek , Srinivasan Vivek J.
Published: May 2020

We critically examine the validity of the cumulant approximation, a major assumption in Diffusing Wave Spectroscopy (DWS) and Diffuse Correlation Spectroscopy (DCS) of blood dynamics, and how it impacts conclusions about red blood cell motion.
SOLUS Project: Bringing Innovation into Breast Cancer Diagnosis and in the Time-Domain Diffuse Optical Field
Authors: Di Sieno Laura , Mora Alberto Dalla , Ferocino Edoardo , Pifferi Antonio , Tosi Alberto , Conca Enrico , Sesta Vincenzo , Giudice Andrea , Ruggeri Alessandro , Tisa Simone , Flocke Alexander , Rosinski Bogdan , Dinten Jean-Marc , Perriollat Mathieu , Savery David , Sportouche Hélène , Arridge Simon , Farina Andrea , Panizza Pietro , Venturini Elena , Gordebeke Peter , Zolda Pamela , Taroni Paola
Published: May 2020

To improve the specificity of breast cancer diagnosis SOLUS combines ultrasound, shear-wave elastography and time-domain diffuse optical tomography in a multimodal imaging system. An innovative compact device for time-domain multi-wavelength diffuse optics was also developed.
Multi-laboratory efforts for the standardization of performance assessment of diffuse optics instruments – the BitMap Exercise
Authors: Lanka Pranav , Yang Lin , Orive-Miguel David , Veesa Joshua Deepak , Tagliabue Susanna , Sudakou Aleh , Samaei Saeed , Forcione Mario , Kovacsova Zuzana , Behera Anurag , Gladytz Thomas , Grosenick Dirk , Hervé Lionel , LoPresti Giuseppe , Cortese Lorenzo , Durduran Turgut , Bejm Karolina , Morawiec Magdalena , Kacprzak Michał , Sawosz Piotr , Grega Anna , Liebert Adam , Belli Antonio , Tachtsidis Ilias , Lange Frederic , Bale Gemma , Baratelli Luca , Gioux Sylvain , Alexander Kalyanov , Wolf Martin , Sekar Sanathana Konugolu Venkata , Zanoletti Marta , Pirovano Ileana , Lacerenza Michele , Qiu Lina , Ferocino Edoardo , Maffeis Giulia , Amendola Caterina , Colombo Lorenzo , Buttafava Mauro , Renna Marco , Di Sieno Laura , Re Rebecca , Farina Andrea , Spinelli Lorenzo , Mora Alberto Dalla , Contini Davide , Taroni Paola , Tosi Alberto , Torricelli Alessandro , Dehghani Hamid , Wabnitz Heidrun , Pifferi Antonio
Published: May 2020

A multi-laboratory exercise, involving 29 diffuse optical instruments, aimed at performance assessment of diffuse optics instruments on standardized protocols is presented. The overarching methodology and future actions will also be discussed.
Longitudinal Monitoring of Cerebral Metabolism in Neonates at Risk for Hypoxic-Ischemic Encephalopathy
Authors: Ferradal Silvina L. , Vyas Rutvi , El-Dib Mohamed , Sutin Jason , Pierce Lara , Morton Sarah , Soul Janet , Lin Pei-Yi , Grant P. Ellen
Published: May 2020

Therapeutic hypothermia decreases cerebral metabolism in neonates at risk for HIE. Here, we quantify cerebral hemodynamics in the first week of life and show significant correlations with neurodevelopmental outcomes at 18 months.