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Article Citation - WoS: 9Citation - Scopus: 10Strain Engineering of Germanium Nanobeams by Electrostatic Actuation(Nature Portfolio, 2019) Ayan, Arman; Turkay, Deniz; Unlu, Buse; Naghinazhadahmadi, Parisa; Oliaei, Samad Nadimi Bavil; Boztug, Cicek; Yerci, SelcukGermanium (Ge) is a promising material for the development of a light source compatible with the silicon microfabrication technology, even though it is an indirect-bandgap material in its bulk form. Among various techniques suggested to boost the light emission efficiency of Ge, the strain induction is capable of providing the wavelength tunability if the strain is applied via an external force. Here, we introduce a method to control the amount of the axial strain, and therefore the emission wavelength, on a suspended Ge nanobeam by an applied voltage. We demonstrate, based on mechanical and electrical simulations, that axial strains over 4% can be achieved without experiencing any mechanical and/or electrical failure. We also show that the non-uniform strain distribution on the Ge nanobeam as a result of the applied voltage enhances light emission over 6 folds as compared to a Ge nanobeam with a uniform strain distribution. We anticipate that electrostatic actuation of Ge nanobeams provides a suitable platform for the realization of the on-chip tunable-wavelength infrared light sources that can be monolithically integrated on Si chips.Article Citation - WoS: 122Citation - Scopus: 114A Multi-Country Test of Brief Reappraisal Interventions on Emotions During the Covid-19 Pandemic(Nature Portfolio, 2021) Wang, Ke; Goldenberg, Amit; Dorison, Charles A.; Miller, Jeremy K.; Uusberg, Andero; Lerner, Jennifer S.; Moshontz, HannahThe COVID-19 pandemic has increased negative emotions and decreased positive emotions globally. Left unchecked, these emotional changes might have a wide array of adverse impacts. To reduce negative emotions and increase positive emotions, we tested the effectiveness of reappraisal, an emotion-regulation strategy that modifies how one thinks about a situation. Participants from 87 countries and regions (n = 21,644) were randomly assigned to one of two brief reappraisal interventions (reconstrual or repurposing) or one of two control conditions (active or passive). Results revealed that both reappraisal interventions (vesus both control conditions) consistently reduced negative emotions and increased positive emotions across different measures. Reconstrual and repurposing interventions had similar effects. Importantly, planned exploratory analyses indicated that reappraisal interventions did not reduce intentions to practice preventive health behaviours. The findings demonstrate the viability of creating scalable, low-cost interventions for use around the world.Article Citation - WoS: 8Citation - Scopus: 9Urinalysis of Individuals With Renal Hyperfiltration Using Atr-Ftir Spectroscopy(Nature Portfolio, 2022) Kurultak, Ilhan; Sarigul, Neslihan; Kodal, Nil Su; Korkmaz, FilizAbnormal increased glomerular filtration rate (GFR), otherwise known as renal hyperfiltration (RHf), is associated with an increased risk of chronic kidney disease and cardiovascular mortality. Although it is not considered as a disease alone in medicine today, early detection of RHf is essential to reducing risk in a timely manner. However, detecting RHf is a challenge since it does not have a practical biochemical marker that can be followed or quantified. In this study, we tested the ability of ATR-FTIR spectroscopy to distinguish 17 individuals with RHf (hyperfiltraters; RHf (+)), from 20 who have normal GFR (normofiltraters; RHf(-)), using urine samples. Spectra collected from hyperfiltraters were significantly different from the control group at positions 1621, 1390, 1346, 933 and 783/cm. Intensity changes at these positions could be followed directly from the absorbance spectra without the need for pre-processing. They were tentatively attributed to urea, citrate, creatinine, phosphate groups, and uric acid, respectively. Using principal component analysis (PCA), major peaks of the second derivative forms for the classification of two groups were determined. Peaks at 1540, 1492, 1390, 1200, 1000 and 840/cm were significantly different between the two groups. Statistical analysis showed that the spectra of normofiltraters are similar; however, those of hyperfiltraters show diversity at multiple positions that can be observed both from the absorbance spectra and the second derivative profiles. This observation implies that RHf can simultaneously affect the excretion of many substances, and that a spectroscopic analysis of urine can be used as a rapid and non-invasive pre-screening tool.Data Paper Citation - WoS: 2Citation - Scopus: 2The Psychological Science Accelerator's Covid-19 Rapid-Response Dataset(Nature Portfolio, 2023) Buchanan, Erin M.; Lewis, Savannah C.; Paris, Bastien; Forscher, Patrick S.; Pavlacic, Jeffrey M.; Beshears, Julie E.; Primbs, Maximilian A.In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing manipulations on behavioral intentions and affective measures. The data collected (April to October 2020) included specific measures for each experimental study, a general questionnaire examining health prevention behaviors and COVID-19 experience, geographical and cultural context characterization, and demographic information for each participant. Each participant started the study with the same general questions and then was randomized to complete either one longer experiment or two shorter experiments. Data were provided by 73,223 participants with varying completion rates. Participants completed the survey from 111 geopolitical regions in 44 unique languages/dialects. The anonymized dataset described here is provided in both raw and processed formats to facilitate re-use and further analyses. The dataset offers secondary analytic opportunities to explore coping, framing, and self-determination across a diverse, global sample obtained at the onset of the COVID-19 pandemic, which can be merged with other time-sampled or geographic data.Article Citation - WoS: 23Citation - Scopus: 26Mesenchymal Stem Cells Promote Spermatogonial Stem/Progenitor Cell Pool and Spermatogenesis in Neonatal Mice in Vitro(Nature Portfolio, 2022) Onen, Selin; Kose, Sevil; Yersal, Nilgun; Korkusuz, PetekPrepubertal cancer treatment leads to irreversible infertility in half of the male patients. Current in vitro spermatogenesis protocols and cryopreservation techniques are inadequate to expand spermatogonial stem/progenitor cells (SSPC) from testicles. Bone marrow derived mesenchymal stem cells (BM-MSC) bearing a close resemblance to Sertoli cells, improved spermatogenesis in animal models. We asked if a co-culture setup supported by syngeneic BM-MSC that contributes to the air-liquid interphase (ALI) could lead to survival, expansion and differentiation of SSPCs in vitro. We generated an ALI platform able to provide a real-time cellular paracrine contribution consisting of syngeneic BM-MSCs to neonatal C57BL/6 mice testes. We aimed to evaluate the efficacy of this culture system on SSPC pool expansion and spermatogenesis throughout a complete spermatogenic cycle by measuring the number of total germ cells (GC), the undifferentiated and differentiating spermatogonia, the spermatocytes and the spermatids. Furthermore, we evaluated the testicular cell cycle phases, the tubular and luminal areas using histochemical, immunohistochemical and flow cytometric techniques. Cultures in present of BM-MSCs displayed survival of ID4(+) spermatogonial stem cells (SSC), expansion of SALL4(+) and OCT4(+) SSPCs, VASA(+) total GCs and Ki67(+) proliferative cells at 42 days and an increased number of SCP3(+) spermatocytes and Acrosin(+) spermatids at 28 days. BM-MSCs increased the percentage of mitotic cells within the G2-M phase of the total testicular cell cycle increased for 7 days, preserved the cell viability for 42 days and induced testicular maturation by enlargement of the tubular and luminal area for 42 days in comparison to the control. The percentage of PLZF(+) SSPCs increased within the first 28 days of culture, after which the pool started to get smaller while the number of spermatocytes and spermatids increased simultaneously. Our findings established the efficacy of syngeneic BM-MSCs on the survival and expansion of the SSPC pool and differentiation of spermatogonia to round spermatids during in vitro culture of prepubertal mice testes for 42 days. This method may be helpful in providing alternative cures for male fertility by supporting in vitro differentiated spermatids that can be used for round spermatid injection (ROSI) to female oocyte in animal models. These findings can be further exploited for personalized cellular therapy strategies to cure male infertility of prepubertal cancer survivors in clinics.Correction A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic (vol 5, pg 1089, 2021)(Nature Portfolio, 2022) Wang, Ke; Goldenberg, Amit; Dorison, Charles A.; Miller, Jeremy K.; Uusberg, Andero; Lerner, Jennifer S.; Moshontz, Hannah[No Abstract Available]Article Citation - WoS: 344Citation - Scopus: 356A New Artificial Urine Protocol To Better Imitate Human Urine(Nature Portfolio, 2019) Sarigul, Neslihan; Korkmaz, Filiz; Kurultak, IlhanArtificial urine has many advantages over human urine for research and educational purposes. By closely mimicking healthy individuals' urine, it may also be important in discovering novel biomarkers. However, up until now, there has not been any specific protocol to prove the similarity in terms of the chemical composition at the molecular level. In this study, a new artificial urine protocol is established to mimics the urine of healthy individuals. The multi-purpose artificial urine (MP-AU) presented here is compared with two other protocols most cited in literature. Furthermore, these three protocols are also compared with samples from 28 healthy young individuals. To do so, attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) is used, according to which MP-AU shows a significantly close similarity with human urine. In formulating MP-AU, the infrared spectra of nine compounds is provided, making possible the band assignment of some absorption bands to certain compounds. Given its properties, the MP-AU protocol introduced here is both economical and practical, making it useful when designing comparative-controlled experiments.Article Citation - WoS: 27Citation - Scopus: 28Microbial Community of Soda Lake Van as Obtained From Direct and Enriched Water, Sediment and Fish Samples(Nature Portfolio, 2021) Omeroglu, Esra Ersoy; Sudagidan, Mert; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Ozalp, Veli CengizSoda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.Article Author Correction: Using Urine Ftir Spectra To Screen Autism Spectrum Disorder(Nature Portfolio, 2024) Sarigul, Neslihan; Bozatli, Leyla; Kurultak, Ilhan; Korkmaz, Filiz[No Abstract Available]Article Citation - WoS: 6Citation - Scopus: 6Using urine FTIR spectra to screen autism spectrum disorder(Nature Portfolio, 2023) Sarigul, Neslihan; Bozatli, Leyla; Kurultak, Ilhan; Korkmaz, FilizAutism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder caused by multiple factors, lacking clear biomarkers. Diagnosing ASD still relies on behavioural and developmental signs and usually requires lengthy observation periods, all of which are demanding for both clinicians and parents. Although many studies have revealed valuable knowledge in this field, no clearly defined, practical, and widely acceptable diagnostic tool exists. In this study, 26 children with ASD (ASD+), aged 3-5 years, and 26 sex and age-matched controls are studied to investigate the diagnostic potential of the Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy. The urine FTIR spectrum results show a downward trend in the 3000-2600/cm region for ASD+ children when compared to the typically developing (TD) children of the same age. The average area of this region is 25% less in ASD+ level 3 children, 29% less in ASD+ level 2 children, and 16% less in ASD+ level 1 children compared to that of the TD children. Principal component analysis was applied to the two groups using the entire spectrum window and five peaks were identified for further analysis. The correlation between the peaks and natural urine components is validated by artificial urine solutions. Less-than-normal levels of uric acid, phosphate groups, and ammonium (NH4+) can be listed as probable causes. This study shows that ATR-FTIR can serve as a practical and non-invasive method to screen ASD using the high-frequency region of the urine spectrum.
