bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk Factors for 30- and 90-Day Readmissions Due To Surgical Site Infection Following Posterior Lumbar Fusion
Authors: Taree Amir , Mikhail Christopher M. , Markowitz Jonathan , Ranson William A. , Choi Brian , Schwartz John T. , Cho Samuel K.
Published: October 2020

Study Design:

This was a retrospective cohort study.

Objective:

Identify the independent risk factors for 30- and 90-day readmission because of surgical site infection (SSI) in patients undergoing elective posterior lumbar fusion (PLF).

Summary of Background Data:

SSI is a significant cause of morbidity in the 30- and 90-day windows after hospital discharge. There remains a gap in the literature on independent risk factors for readmission because of SSI after PLF procedures. In addition, readmission for SSI after spine surgery beyond the 30-day postoperative period has not been well studied.

Methods:

A retrospective analysis was performed on data from the 2012 to 2014 Healthcare Cost and Utilization Project Nationwide Readmissions Database. The authors identified 65,121 patients who underwent PLF. There were 191 patients (0.30%) readmitted with a diagnosis of SSI in the 30-day readmission window, and 283 (0.43%) patients readmitted with a diagnosis of SSI in the 90-day window. Baseline patient demographics and medical comorbidities were assessed. Bivariate and multivariate analyses were performed to examine the independent risk factors for readmission because of SSI.

Results:

In the 30-day window after discharge, this study identified patients with liver disease, uncomplicated diabetes, deficiency anemia, depression, psychosis, renal failure, obesity, and Medicaid or Medicare insurance as higher risk patients for unplanned readmission with a diagnosis of SSI. The study identified the same risk factors in the 90-day window with the addition of diabetes with chronic complications, chronic pulmonary disease, and pulmonary circulation disease.

Conclusions:

Independent risk factors for readmission because of SSI included liver disease, uncomplicated diabetes, obesity, and Medicaid insurance status. These findings suggest that additional intervention in the perioperative workup for patients with these risk factors may be necessary to lower unplanned readmission because of SSI after PLF surgery.
EGFR-mutant NSCLC: emerging novel drugs
Authors: Ye Lingyun , Chen Xiaoxia , Zhou Fei
Published: October 2020

Purpose of review

Despite the significant advances in EGFR-mutant nonsmall cell lung cancer (NSCLC), some challenges remain. One of the permanent and inevitable issues is the emergence of acquired resistance. Therefore, blocking the activation of EGFR pathway and overcoming drug resistance with novel agents are still in high demand. Here, we review the development of novel drugs in EGFR-mutant, advanced NSCLC, including targeting EGFR exon 20 insertion (EGFR20ins), and novel role of epidermal growth factor receptor, tyrosine kinase inhibitor (EGFR-TKIs) in early-stage NSCLC.

Recent findings

EGFR-TKIs as adjuvant therapy or neoadjuvant therapy in patients with early-stage NSCLC with EGFR-sensitizing mutations have shown promising efficacy. The resistance mechanisms of third-generation EGFR-TKIs can be divided into two types: EGFR dependent and EGFR independent. Several clinical trials have demonstrated that the addition of MET inhibitors to EGFR-TKIs was an effective option for patients who had acquired resistance to EGFR-TKIs caused by hepatocyte growth factor receptor gene (MET) amplification or overexpression. Novel compounds that selectively and potently inhibit EGFR20ins are being investigated in phase III studies.

A better characterization and understanding of resistance mechanisms to first-line osimertinib and adjuvant osimertinib is helpful to guide further treatment.
Ultrasound increases the success rate of spinal needle placement through the epidural needle during combined spinal-epidural anaesthesia
Authors: Tao Bingdong , Liu Kun , Ding Mengmeng , Xue Hang , Li Xingyue , Zhao Ping
Published: October 2020

BACKGROUND

Combined spinal-epidural anaesthesia (CSEA) using a needle-through-needle technique is currently widely used. However, successful epidural needle placement does not mean a successful spinal needle placement during CSEA. Whether ultrasound assistance could increase the first-pass success rate of spinal needle placement for CSEA remains unknown.

OBJECTIVE

The aim of this study was to investigate if ultrasound assistance could increase the first-pass success rate of spinal needle placement through the epidural needle during CSEA performed by experienced anaesthesiologists in patients undergoing caesarean section.

DESIGN

A prospective, randomised, double-blind study.

SETTING

Single centre, Department of Anaesthesiology, Shengjing Hospital, China Medical University, China, from June 2019 to September 2019.

PATIENTS

A total of 185 patients (aged 24 years to 52 years, American Society of Anesthesiologists grade (ASA) II-III, 38 to 40 weeks gestation) scheduled to undergo elective caesarean section under CSEA were enrolled.

INTERVENTION

The patients were randomised to either an ultrasound group (patients received a preprocedural ultrasound scan, and the puncture site was identified by ultrasound imaging) and a palpation group (patients received a sham procedural ultrasound scan, and the puncture site was identified by conventional palpation).

MAIN OUTCOME MEASURES

The primary outcome measure was the first-pass success rate for spinal needle placement through the epidural needle. Secondary outcome measures were total duration of CSEA, time required for successful epidural needle and spinal needle placement, number of epidural needle redirections and complications.

RESULTS

Preprocedural ultrasound imaging significantly increased the first-pass success rate of spinal needle placement through the epidural needle compared with conventional palpation (93.8 vs. 68.8%, P < 0.001). Preprocedural ultrasound imaging also decreased the total duration of CSEA (186.9 ± 37.1 vs. 213 ± 60.4 s, P = 0.0015) and the time required for successful spinal needle placement (78.3 ± 22.9 vs. 100.1 ± 53.7 s, P < 0.01) compared with conventional palpation. Fewer patients in the ultrasound group needed epidural needle redirections during the spinal needle placement procedure than in the palpation group (four patients vs. 20 patients, P < 0.01).

CONCLUSION

For experienced anaesthesiologists, preprocedural ultrasound imaging significantly increased the first-pass success rate of spinal needle placement through the epidural needle for obstetric patients undergoing caesarean section under CSEA.

TRIAL REGISTRATION

chictr.org.cn, identifier: ChiCTR1900024132
Local and regional therapy considerations after preoperative therapy in patients with breast cancer
Authors: Untch Michael
Published: October 2020

Purpose of review

The starting point of neoadjuvant therapy was to use preoperative chemotherapy in order to provide surgeons and radiotherapists with the possibility of local treatment in patients with locally advanced, primary inoperable or inflammatory disease. Since then, this treatment approach has dramatically evolved and is now a standard of care in patients with high-risk early breast cancer.

Recent findings

The role of surgery after neoadjuvant therapy is to remove residual disease in the breast and or in the lymph nodes and to provide further treatment possibilities according to pathohistologic findings at surgery.

Innovative medical treatments are now being used for neoadjuvant treatment in order to reduce the extent of locoregional surgery in the breast and the axilla and also to adjust further medical treatment after neoadjuvant therapy and surgery.
Use of presbyopia-correcting intraocular lenses in patients with prior corneal refractive surgery
Authors: Moshirfar Majid , Thomson Andrew C. , Thomson Robert J. , Martheswaran Tanisha , McCabe Shannon E.
Published: October 2020

Purpose of review

Corneal refractive surgery has achieved spectacle-free vision for millions of patients, but this aging population is now developing cataracts. Many of these patients may wish to avoid reliance on glasses after cataract surgery. Presbyopia-correcting intraocular lenses (IOLs) offer a solution, but corneal changes after refractive surgery may compound higher order aberrations and dysphotopic symptoms associated with these IOLs. This review aims to discuss potential factors that could aid in determining suitable postkeratorefractive candidates for presbyopia-correcting IOLs.

Recent findings

Studies investigating which preoperative measures influence outcomes are lacking. The few studies that have examined presbyopia-correcting IOLs in postkeratorefractive patients report that satisfactory outcomes are possible. However, recommendations for preoperative thresholds appear limited to expert opinion and studies involving virgin corneas.

As the number of presbyopia-correcting IOLs and postkeratorefractive patients grows, continued investigation into relevant preoperative factors and appropriate IOLs is required to make evidence-based decisions. The current literature shows that with rigorous counseling and appropriate patient selection, presbyopia-correcting IOLs can provide postkeratorefractive patients with satisfactory results and spectacle independence. In addition, the development of postoperative modifiable IOLs may prove to be the preferred option.
Retained Granulation Cuff as a Complication of Indwelling Pleural Catheter Removal
Authors: Gilbert Christopher R. , Wilshire Candice L. , Gorden Jed A.
Published: October 2020

Recurrent pleural effusions can be managed with indwelling tunneled pleural catheters (IPC), with some patients undergoing IPC removal after appropriate palliation has occurred. Little data exists regarding complications related to IPC removal. We report on retained granulation cuffs after successful IPC removal. We identified 122 IPC removals of which 6 (4.9%) were complicated by retained granulation cuff. No additional procedures or need for retrieval were identified over a median follow-up time of 423.5 (IQR–204-1489) days. Clinicians should be aware of this potential complication, but that retained granulation cuffs appear to offer no sequelae and aggressive interventions for retrieval/removal are likely not warranted.
Imprint Cytology of Thoracoscopic Pleural Biopsy Tissue for Early Etiological Diagnosis of Pleural Effusion
Authors: Gupta Richa , Arul Ashwin Oliver , Sasikumar Jebin Roger , Prabhu Anne Jennifer , James Prince
Published: October 2020

Thoracoscopic pleural biopsy provides the highest diagnostic yield in both malignant and tubercular pleural effusions. However histopathologic report takes 3 to 5 days to provide the diagnosis, resulting in a delay of further management plans like pleurodesis or chest tube removal. Imprint cytology of biopsy tissue can provide early information about the etiological diagnosis. Thus, we conducted this pilot study in 66 patients of exudative pleural effusions undergoing medical thoracoscopy. One or 2 biopsy pieces obtained during medical thoracoscopy from pleural nodules were used to prepare imprint cytology slides in the thoracoscopy suite. In comparison to thoracoscopic pleural biopsy, the diagnostic yield of imprint cytology of pleural tissue was 92% (49 of 53 cases) in cases of malignant pleural effusion and 75% (9 of 12 cases) in cases of tuberculosis pleural effusions. Imprint cytology provided a definite idea about the type of diagnosis, about 2.5 days before the histopathology results. By providing early etiological diagnosis, it may also decrease the duration of hospital stay and health care expenditure. A large prospective trial has been planned in our center to confirm this hypothesis.
The Use of B-Cell Polysome Profiling to Validate Novel RPL5 (uL18) and RPL26 (uL24) Variants in Diamond-Blackfan Anemia
Authors: Ludlow Alexander , George Nicholas , Glassford Megan , Udenberg Katie , Hannibal Mark C. , Schwalm Carla , Scott Katie , Rothstein Thomas L. , Singh Sharon A.
Published: October 2020

Diamond-Blackfan anemia (DBA) is a rare bone marrow failure syndrome usually caused by heterozygous variants in ribosomal proteins (RP) and which leads to severe anemia. Genetic studies in DBA rely primarily on multigene panels that often result in variants of unknown significance. Our objective was to optimize polysome profiling to functionally validate new large subunit RP variants. We determined the optimal experimental conditions for B-cell polysome profiles then performed this analysis on 2 children with DBA and novel missense RPL5 (uL18) and RPL26 (uL24) variants of unknown significance. Both patients had reduced 60S and 80S fractions when compared with an unaffected parent consistent with a large ribosomal subunit defect. Polysome profiling using primary B-cells is an adjunctive tool that can assist in validation of large subunit RP variants of uncertain significance. Further studies are necessary to validate this method in patients with known DBA mutations, small RP subunit variants, and silent carriers.
Adiposity in Survivors of Cancer in Childhood: How is it Measured and Why Does it Matter?
Authors: Guolla Louise , Morrison Katherine M. , Barr Ronald D.
Published: October 2020

Survival of cancer in childhood is increasingly common with modern therapeutic protocols but leads frequently to adverse long-term impacts on health, including metabolic and cardiovascular disease. Changes in body composition, especially an increase in fat mass and a decrease in muscle mass, are found early in patients with pediatric cancer, persist long after treatment has been completed and seem to contribute to the development of chronic disease. This review details the effects of such changes in body composition and reviews the underlying pathophysiology of the development of sarcopenic obesity and its adverse metabolic impact. The authors discuss the particular challenges in identifying obesity accurately in survivors of pediatric cancer using available measurement techniques, given that common measures, such as body mass index, do not distinguish between muscle and adipose tissue or assess their distribution. The authors highlight the importance of a harmonized approach to the assessment of body composition in pediatric cancer survivors and early identification of risk using “gold-standard” measurements. This will improve our understanding of the significance of adiposity and sarcopenia in this population, help identify thresholds predictive of metabolic risk, and ultimately prevent or ameliorate the long-term metabolic and cardiovascular impacts on health experienced by survivors of cancer in childhood.
Changes in the Trend of Sexually Acquired Chlamydia Infections in Sweden and the Role of Testing: A Time Series Analysis
Authors: Veličko Inga , Ploner Alexander , Sparén Pär , Herrmann Björn , Marions Lena , Kühlmann-Berenzon Sharon
Published: October 2020

Background

We investigated the notification trends of sexually acquired chlamydia (chlamydia) and its association with testing in Sweden before (1992–2004) and after (2009–2018) the discovery of a new variant of Chlamydia trachomatis (nvCT).

Methods

We applied monthly time series analysis to study chlamydia trends and annual time series to study chlamydia rates adjusted for testing. We analyzed incidence nationally and by county group (based on able and unable to detect nvCT at time of discovery).

Results

We present data on 606,000 cases of chlamydia and 9.9 million persons tested. We found a U-shaped chlamydia trend during the period 1992–2004, with an overall increase of 83.7% from 1996 onward. The period 2009–2018 began with a stable trend at a high incidence level followed by a decrease of 19.7% during the period 2015–2018. Peaks were seen in autumn and through during winter and summer. Similar results were observed by groups of county, although with varying levels of increase and decrease in both periods. Furthermore, increased testing volume was associated with increased chlamydia rates during the first period (P = 0.019) but not the second period.

Conclusions

Our results showed that chlamydia trends during the period 2009–2018 were not driven by testing, as they were during the period 1992–2004. This suggests less biased notified chlamydia rates and thus possibly a true decrease in chlamydia incidence rates. It is important to adjust case rates for testing intensity, and future research should target other potential factors influencing chlamydia rates.
Implications of HIV Self-Testing for Other Sexually Transmissible Infection Testing and Broader Sexual Health Needs: A Mixed-Methods Study of Gay and Bisexual Men in Australia
Authors: Leitinger David , Ryan Kathleen , Wilkinson Anna Lee , Pedrana Alisa , Hellard Margaret , Stoové Mark
Published: October 2020

Background

Although HIV self-tests can support frequent HIV testing, their impact on attending clinics for other sexually transmissible infection (STI) testing and sexual health care is largely unknown. We explored intentions to use HIV self-tests and how this might affect patterns of attending sexual health services among gay, bisexual, and other men who have sex with men (GBM) in Victoria, Australia.

Methods

Gay, bisexual, and other men who have sex with men self-completed an online survey between March 10 and June 10, 2019. Among GBM reporting lifetime HIV testing and intentions to self-test at least once annually, we used logistic regression to identify correlates of intending to replace clinic-based HIV testing with self-tests. Qualitative interviews with purposively selected survey participants undertaken between May and June 2019 explored the implications of self-testing on clinic-based sexual health care.

Results

Of the 279 survey participants, 79 (29%) reported they would replace most or all clinic-based HIV tests with self-tests, with longer time since last testing for HIV and younger age associated with reporting this outcome in the multivariate analysis. Qualitative interviews revealed different perceived roles for self-tests and clinic-based testing, and the importance of integrating HIV self-tests within broader sexual health routines.

Conclusions

Although GBM see a distinct role for HIV self-testing, its rollout will likely result in missed opportunities for clinic-based STI testing and education for some GBM, particularly among younger and less-recently tested GBM. Convenient, non–clinic-based approaches to STI testing are needed alongside support platforms to maximize the benefits of HIV self-testing within comprehensive sexual health routines.
Surgical and Neurological Outcome of Minimally Invasive Thymectomy in Patients With Myasthenia Gravis: An Experience of 100 Cases Over 6 Years at a Tertiary Care Center in North India
Authors: Parshad Rajinder , Verma Eshan , Suhani Suhani , Goyal Vinay , Bhatia Rohit , Sharma Raju , Datta Gupta Siddhartha
Published: October 2020

Background:

Minimally invasive thymectomy (MIT) is emerging as an effective alternative to open thymectomy in the management of patients with myasthenia gravis (MG). The primary objective of our study is to assess the surgical and neurological outcome of MIT in patients with MG.

Materials and Methods:

It is a retrospective evaluation of prospectively collected data of 100 patients with MG, who underwent MIT from April 2012 to January 2018 at a tertiary care center in India. Surgical outcome was assessed for success of minimal invasive approach, conversion, perioperative morbidity, and postoperative hospital course. Neurological outcome was assessed, after at least 1 year of follow-up, according to Myasthenia Gravis Foundation of America postintervention status. Factors predicting complete stable remission (CSR) were evaluated.

Results:

MIT was successfully performed in 98% patients with 2% conversion. There was no mortality. Overall, 10% of patients had perioperative morbidity with 5% having exacerbation of neurological symptoms. Two of these needed postoperative ventilation, whereas 3 recovered on conservative treatment. Median operative time and hospital stay were 140 minutes and 3 days, respectively. At a median follow-up of 47 months, CSR was seen in 20% with improvement in 73.3%. Overall, 63% patients were taken off steroids and patients requiring 3 drugs decreased by 70.7%. There was significant reduction in the dosage of pyridostigmine (P<0.001), prednisolone (P<0.001), and azathioprine (P=0.002) after thymectomy. Milder disease (Myasthenia Gravis Foundation of America class 1 and 2) predicted CSR on multivariate analysis.

Conclusions:

MIT is a safe and effective procedure that leads to improvement in neurological status with significant reduction in number and dosage of medications after thymectomy. Mild disease predicts CSR.
Psychroflexus aurantiacus sp. nov., isolated from soil in the Yellow River Delta wetlands
Authors: Wu Shu-ge , Wang Jing-jing , Wang Jia-ning , Chen Qi , Sheng Duo-hong , Li Yue-zhong
Published: October 2020

A Gram-stain-negative, strictly aerobic, non-motile, orange-coloured bacterium, designated YR1-1T, was isolated from a soil sample collected from the Yellow River Delta wetlands (PR China). Growth was observed at a salinity of 1.0–15.0 % NaCl, 4–45 °C and pH 6.0–9.0. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that YR1-1T represented a member of the genus

Psychroflexus

, with the highest sequence similarity to

Psychroflexus sediminis

YIM-C238T (97.9 %), followed by

Psychroflexus aestuariivivens

(97.1 %) and

Psychroflexus torquis

(96.4 %). The average nucleotide identity and digital DNA–DNA hybridization values between YR1-1T and other closely related type strains of species of the genus

Psychroflexus

were 68.7–86.3% and 17.8–30.9 %. The genome of the strain was 2 899 374 bp in length with 39.8 % DNA G+C content. The predominant fatty acids (>10 %) were iso-C15 : 0 and anteiso-C15 : 0. The major respiratory quinone was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, phospholipid, diphosphatidylglycerol, two unidentified aminolipids and four unidentified lipids. The combined genotypic and phenotypic data indicate that YR1-1T represents a novel species within the genus

Psychroflexus

, for which the name Psychroflexus aurantiacus sp. nov., is proposed. The type strain is YR1-1T (=KCTC 72794T=CGMCC 1.17458T).
Word detection in individual subjects is difficult to probe with fast periodic visual stimulation
Authors: Barnes Lydia , Petit Selene , Badcock Nicholas , Whyte Christopher , Woolgar Alexandra
Published: October 2020

Measuring cognition in single subjects presents unique challenges. Yet individually sensitive measurements offer extraordinary opportunities, from informing theoretical models to enabling truly individualised clinical assessment. Here, we test the robustness of fast, periodic, visual stimulation (FPVS), an emerging method proposed to elicit detectable responses to written words in the electroencephalogram (EEG) of individual subjects. The method is non-invasive, passive, and requires only a few minutes of testing, making it a potentially powerful tool to test comprehension in those who do not speak or who struggle with long testing procedures. In an initial study, Lochy et al. (2015) used FPVS to detect word processing in 8 out of 10 fluent French readers. Here, we attempted to replicate their study in a new sample of ten fluent English readers. Participants viewed rapid streams of pseudo-words with words embedded at regular intervals, while we recorded their EEG. Based on Lochy et al., we expected that words would elicit a steady-state response at the word-presentation frequency (2 Hz) over parieto-occipital electrode sites. However, across 40 datasets (10 participants, two conditions, and two regions of interest - ROIs), only four datasets met the criteria for a unique response to words. This corresponds to a 10% detection rate. We conclude that FPVS should be developed further before it can serve as an individually-sensitive measure of written word processing.
The evolution of two distinct strategies of moth flight
Authors: Aiello Brett R. , Sikandar Usama Bin , Minoguchi Hajime , Bhinderwala Burhanuddin , Hamilton Chris A. , Kawahara Akito Y. , Sponberg Simon
Published: October 2020

Across insects, wing shape and size have undergone dramatic divergence even in closely related sister groups, but we do not yet know morphology changes in tandem with kinematics to support body weight within available aerodynamic power and how the specific force production patterns are linked to changes in behavior. Hawkmoths and wild silkmoths are two such diverse sister families with divergent wing morphology. Using 3d kinematics and quasi-steady aerodynamic modeling, we compare the aerodynamics and the contributions of wing shape, size, and kinematics in 10 moth species. We find that wing movement also diverges between the clades and underlies two distinct strategies for flight. Hawkmoths use wing kinematics, especially high frequencies, to enhance force, but wing morphologies that reduces power. Silkmoths use wing morphology to enhance force, and high amplitude wingstrokes to reduce power. Both strategies converge on similar aerodynamic power and can support similar body mass ranges, but their within-wingstroke force profiles are quite different and linked to the hovering flight of hawkmoths and the bobbing flight of silkmoths. These two groups of moths each fly more like other, distantly related insects than they do each other, demonstrating the convergence and diversity of flapping flight evolution.
SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway
Authors: Chen Da-Yuan , Khan Nazimuddin , Close Brianna J. , Goel Raghuveera K. , Blum Benjamin , Tavares Alexander H. , Kenney Devin , Conway Hasahn L. , Ewoldt Jourdan K. , Kapell Sebastian , Chitalia Vipul C. , Crossland Nicholas A. , Chen Christopher S. , Kotton Darrell N. , Baker Susan C. , Connor John H. , Douam Florian , Emili Andrew , Saeed Mohsan
Published: October 2020

SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we performed global proteomic analysis of the virus-host interface in a newly established panel of phenotypically diverse, SARS-CoV-2-infectable human cell lines representing different body organs. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cell lines and primary-like cardiomyocytes, and found that several pathway components were targeted by SARS-CoV-2 leading to cellular desensitization to interferon. These findings indicate that the suppression of interferon signaling is a mechanism widely used by SARS-CoV-2 in diverse tissues to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19.
Multiomics study of a heterotardigrade,Echinisicus testudo, suggests convergent evolution of anhydrobiosis-related proteins in Tardigrada
Authors: Murai Yumi , Yagi-Utsumi Maho , Fujiwara Masayuki , Tomita Masaru , Kato Koichi , Arakawa Kazuharu
Published: October 2020

Many limno-terrestrial tardigrades can enter an ametabolic state upon desiccation, in which the animals can withstand extreme environments. To date, studies of the molecular mechanism have predominantly investigated the class Eutardigrada, and that in the Heterotardigrada, remains elusive. To this end, we report a multiomics study of the heterotardigradeEchiniscus testudo, which is one of the most desiccation-tolerant species. None of the previously identified tardigrade-specific anhydrobiosis-related genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families of novel abundant heat-soluble proteins and the proteins exhibited structural changes from random coil to α-helix as the water content decreasedin vitro. These characteristics are analogous to those of anhydrobiosis-related protein in eutardigrades, while there is no conservation at the sequence level. Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada.
Differential sensitivity to hypoxia enables shape-based classification of sickle cell disease and trait blood samples
Authors: D’Costa Claudy , Sharma Oshin , Manna Riddha , Singh Minakshi , Samrat  , Singh Srushti , Mahto Anish , Govil Pratiksha , Satti Sampath , Mehendale Ninad , Italia Yazdi , Paul Debjani
Published: October 2020

Differentiating between homozygous (disease) and heterozygous (trait) sickle cell patients is the key to ensuring appropriate long-term disease management. Well-equipped labs needed to perform confirmatory diagnostic tests are not available in endemic areas of most low- and medium-income countries. As a consequence of hemoglobin polymerization, red blood cells (RBCs) become sickle shaped and stiff under hypoxic conditions in sickle cell anemia patients. A simple test such as microscopy, using RBC shape as a biophysical marker, cannot conclusively differentiate between homozygous (disease) and heterozygous (trait) sickle blood. Here, we establish a new paradigm of microscopic diagnosis of sickle cell disease by exploiting differential polymerization of hemoglobin in disease and trait RBCs under controlled, chemically-induced hypoxia in a microfluidic chip. We use a portable smartphone microscope to compare the RBC shape distributions in blood treated with high and low concentrations of the hypoxia-inducing agent to correctly identify 35 blood samples as healthy, sickle cell disease or trait. Finally, we demonstrate our test in remote field locations to enable fast and confirmed diagnosis of sickle cell anemia in resource-limited areas.
The highly evolvable nature of the antibiotic efflux protein TolC limits use of phages and bacterial toxins as antibacterial agents
Authors: Tamer Yusuf Talha , Gaszek Ilona , Rodrigues Marinelle , Coskun Fatma Sevde , Farid Michael , Koh Andrew Y. , Russ William , Toprak Erdal
Published: October 2020

Bacteriophages and bacterial toxins are promising antibacterial agents to treat infections caused by multidrug resistant (MDR) bacteria. In fact, bacteriophages have recently been successfully used to treat life-threatening infections caused by MDR bacteria [1–3]. One potential problem with using these antibacterial agents is the evolution of resistance against them in the long term. Here, we studied the fitness landscape of theEscherichia coliTolC protein, an outer membrane protein that is exploited by a pore forming toxin called colicin E1 and by TLS-phage [4, 5]. By systematically assessing the distribution of fitness effects (DFEs) of ~9,000 single amino acid replacements in TolC using either positive (antibiotics and bile salts) or negative (colicin E1 and TLS-phage) selection pressures, we quantified evolvability of the TolC. We demonstrated that the TolC is highly optimized for the efflux of antibiotics and bile salts. In contrast, under colicin E1 and TLS phage selection, TolC sequence is very sensitive to mutation. Our findings suggest that TolC is a highly evolvable target limiting the potential clinical use of bacteriophages and bacterial toxins.
Magnitude and kinetics of T cell and antibody responses during H1N1pdm09 infection in outbred and inbred Babraham pigs
Authors: Edmans Matthew , McNee Adam , Porter Emily , Vatzia Eleni , Paudyal Basu , Martini Veronica , Gubbins Simon , Francis Ore , Harley Ross , Thomas Amy , Burt Rachel , Morgan Sophie , Fuller Anna , Sewell Andrew ,   sLoLA Influenza Dynamics consortium, Charleston Bryan , Bailey Mick , Tchilian Elma
Published: October 2020

We have used the pig, a large natural host animal for influenza with many physiological similarities to humans, to characterize αβ, γδ T cell and antibody (Ab) immune responses to the 2009 pandemic H1N1 virus infection. We evaluated the kinetic of virus infection and associated response in inbred Babraham pigs with identical MHC (Swine Leucocyte Antigen) and compared them to commercial outbred animals. High level of nasal virus shedding continued up to day 4-5 post infection followed by a steep decline and clearance of virus by day 9. Adaptive T cell and Ab responses were detectable from day 5-6 post infection reaching a peak at 9-14 days. γδ cells produced cytokinesex vivoat day 2 post infection, while virus specific IFNγ producing γδ T cells were detected from day 7 post infection. Analysis of NP tetramer specific and virus specific CD8 and CD4 T cells in blood, lung, lung draining lymph nodes and broncho-alveolar lavage (BAL) showed clear differences in cytokine production between these tissues. BAL contained the most highly activated CD8, CD4 and γδ cells producing large amounts of cytokines, which likely contribute to elimination of virus. The weak response in blood did not reflect the powerful local lung immune responses. The immune response in the Babraham pig following H1N1pdm09 influenza infection was comparable to that of outbred animals. The ability to utilize these two swine models together will provide unparalleled power to analyse immune responses to influenza.
Vertical-junction Photodiodes for Smaller Pixels in Retinal Prostheses
Authors: Huang Tiffany W , Kamins Theodore I , Chen Zhijie Charles , Wang Bing-Yi , Bhuckory Mohajeet , Galambos Ludwig , Ho Elton , Ling Tong , Afshar Sean , Shin Andrew , Zuckerman Valentina , Harris James S , Mathieson Keith , Palanker Daniel
Published: October 2020

Objective

To restore central vision in patients with atrophic age-related macular degeneration, we replace the lost photoreceptors with photovoltaic pixels, which convert light into current and stimulate the secondary retinal neurons. Clinical trials demonstrated prosthetic acuity closely matching the sampling limit of the 100 μm pixels, and hence smaller pixels are required for improving visual acuity. However, with smaller flat bipolar pixels, the electric field penetration depth and the photodiode responsivity significantly decrease, making the device inefficient. Smaller pixels may be enabled (1) by increasing the diode responsivity using vertical p-n junctions and (2) by directing the electric field vertically using 3-D electrodes. Here, we demonstrate such novel photodiodes and test the retinal stimulation in a vertical electric field.

Approach

Arrays of silicon photodiodes of 55, 40, 30, and 20 μm in width, with vertical p-n junctions, were fabricated. The electric field in the retina was directed vertically by a common return electrode at the edge of the devices. Optical and electronic performance of the diodes was characterized in-vitro, and retinal stimulation threshold measured by recording the visually evoked potentials (VEPs) in rats with retinal degeneration.

Main results

The photodiodes exhibited sufficiently low dark current (<10 pA) and responsivity at 880 nm wavelength as high as 0.51 A/W, with 85% internal quantum efficiency, independent of pixel size. Field mapping in saline demonstrated uniformity of the pixel performance in the array. The full-field stimulation threshold was as low as 0.057±0.029 mW/mm2with 10 ms pulses, independent of pixel size.

Significance

Photodiodes with vertical p-n junctions demonstrated excellent charge collection efficiency independent of pixel size, down to 20 μm. Vertically-oriented electric field provides a stimulation threshold that is independent of pixel size. These results are the first steps in validation of the feasibility of scaling down the photovoltaic pixels for subretinal stimulation.
Engineering Gac/Rsm signaling cascade for optogenetic induction of pathogenicity switch inPseudomonas aeruginosa
Authors: Cheng Xinyi , Pu Lu , Fu Shengwei , Xia Aiguo , Huang Shuqiang , Ni Lei , Xing Xiaochen , Yang Shuai , Jin Fan
Published: October 2020

Bacterial pathogens operate by tightly controlling the pathogenicity to facilitate invasion and survival in host. While small molecule inducers can be designed to modulate pathogenicity to perform studies of pathogen-host interaction, these approaches, due to the diffusion property of chemicals, may have unintended, or pleiotropic effects that can impose limitations on their use. By contrast, light provides superior spatial and temporal resolution. Here, using optogenetics we reengineered GacS of the opportunistic pathogenPseudomonas aeruginosa, signal transduction protein of the global Gac/Rsm cascade which is of central importance for regulation of infection factors. The resultant protein YGS24 displayed significant light-dependent activity of GacS kinases inPseudomonas aeruginosa. When introduced inCaenorhabditis eleganshost systems, YGS24 stimulated the pathogenicity of PAO1 in BHI and of PA14 in SK medium progressively upon blue-light exposure. This optogenetic system provides an accessible way to spatiotemporally control bacterial pathogenicity in defined host even specific tissues to develop new pathogenesis systems, which may in turn expedite development of innovative therapeutics.
Longitudinal ultrasonic dimensions and parametric solid models of the gravid uterus and cervix
Authors: Louwagie Erin , Carlson Lindsey , Over Veronica , Mao Lu , Fang Shuyang , Westervelt Andrea , Vink Joy , Hall Timothy , Feltovich Helen , Myers Kristin
Published: October 2020

Tissue mechanics is central to pregnancy, during which maternal anatomic structures undergo continuous remodeling to serve a dual function to first protect the fetus in utero while it develops and then facilitate its passage out. In this study of normal pregnancy using biomechanical solid modeling, we used standard clinical ultrasound images to obtain measurements of structural dimensions of the gravid uterus and cervix throughout gestation. 2-dimensional ultrasound images were acquired from the uterus and cervix in 30 pregnant subjects in supine and standing positions at four time points during pregnancy (8-14, 14-16, 22-24, and 32-34 weeks). Offline, three observers independently measured from the images of multiple anatomic regions. Statistical analysis was performed to evaluate inter-observer variance, as well as effect of gestational age, gravity, and parity on maternal geometry. A parametric solid model developed in the Solidworks computer aided design (CAD) software was used to convert ultrasonic measurements to a 3-dimensional solid computer model, from which estimates of uterine and cervical volumes were made. This parametric model was compared against previous 3-dimensional solid models derived from magnetic resonance frequency images in pregnancy. In brief, we found several anatomic measurements easily derived from standard clinical imaging are reproducible and reliable, and provide sufficient information to allow biomechanical solid modeling. This structural dataset is the first, to our knowledge, to provide key variables to enable future computational calculations of tissue stress and stretch in pregnancy, making it possible to characterize the biomechanical milieu of normal pregnancy. This vital dataset will be the foundation to understand how the uterus and cervix malfunction in pregnancy leading to adverse perinatal outcomes.
Transcriptome analysis reveals the main metabolic pathway of c-GMP induced by salt stress in tomato seedlings
Authors: Zhu Xiaolin , Su Meifei , Wei Xiaohong , Long Yu , Wang Baoqiang , Wang Xian
Published: October 2020

Tomato is a model crop, as well as important food worldwide. In the arid areas, aggravation of soil salinity has become the primary problem that threatens the high yield in tomato production. As a second messenger substance, cyclic guanosine monophosphate (c-GMP) plays an indispensable role in plant response to salt stress through regulating cell processes to promote plant growth and development. However, this mechanism has not been fully explored in tomato seedlings. In this experiment, the tomato seeds were cultured in distilled water (CK), 20 μM c-GMP (T1), 50 mM NaCl (T2), 20 μM c-GMP + 50 mM NaCl (T3). The results show that 20 μM c-GMP effectively alleviated the inhibition of 50 mM NaCl on tomato growth and development, inducing the expression of 1580 DEGs. 95 DEGs were up-regulated and 442 DEGs were down-regulated (CK vs T1), whereas in the T2 vs T3 comparison 271 DEGs were up-regulated and 772 DEGs were down-regulated. Based on KEGG analysis, the majority of DEGs were involved in metabolism; exogenous c-GMP induced significant enrichment of pathways associated with carbohydrates, phenylpropanoids and fatty acid metabolism. MostPMEs, acCoA, PAL, PODs, FADs, andADwere up-regulated, andGAPDHs, PL, PG, BXL4, andβ-Gwere down-regulated, which reduced susceptibility of tomato seedlings to salt and promoted their salt adaptation. The application of c-GMP promoted soluble sugar, flavonoids and lignin content, reduced accumulation of MDA, and enhanced the activity of POD. Thus, our results provide insights into the molecular mechanisms associated with salt tolerance of tomato seedlings.
A GO catalogue of human DNA-binding transcription factors
Authors: Lovering Ruth C. , Gaudet Pascale , Acencio Marcio L. , Ignatchenko Alex , Jolma Arttu , Fornes Oriol , Kuiper Martin , Kulakovskiy Ivan V. , Lægreid Astrid , Martin Maria J. , Logie Colin
Published: October 2020

DNA-binding transcription factors recognise genomic addresses, specific sequence motifs in gene regulatory regions, to control gene transcription. A complete and reliable catalogue of all DNA-binding transcription factors is key to investigating the delicate balance of gene regulation in response to environmental and developmental stimuli. The need for such a catalogue of proteins is demonstrated by the many lists of DNA-binding transcription factors that have been produced over the past decade.

The COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) Consortium brought together experts in the field of transcription with the aim of providing high quality and interoperable gene regulatory data. The Gene Ontology (GO) Consortium provides strict definitions for gene product function, including factors that regulate transcription. The collaboration between the GREEKC and GO Consortia has enabled the application of those definitions to produce a new curated catalogue of human DNA-binding transcription factors, that can be accessed athttps://www.ebi.ac.uk/QuickGO/targetset/dbTF.

In addition, this curation effort has led to the GO annotation of almost sixty thousand DNA-binding transcription factors in over a hundred species. Thus, this work will aid researchers investigating the regulation of transcription in both biomedical and basic science.
Production of HPV16 capsid proteins in suspension cultures of human epithelial cells
Authors: Sakauchi Dirce , Sasaki Erica Akemi Kavati , de Oliveira Bou Anni Fernanda , Cianciarullo Aurora Marques
Published: October 2020

Human papillomavirus (HPV) infection is a leading cause of morbidity and mortality in women worldwide. The virus is associated with benign warts and a broad spectrum of malignancies, including cervical cancer, considered a disease of high clinical relevance, especially in developing countries. In this study we developed the production of recombinant proteins HPV16 L1 and HPV16 L2 in human cells in suspension (293-F), which were transiently co-transfected with the pUF3/L1h and pUF3/L2h vectors. Expressions of recombinant HPV16 L1 and L2 capsid proteins was detected by laser scanning confocal microscopy and flow cytometry. Both proteins were identified intracellularly in the nucleus and cytoplasm of cells. The presence of these heterologous proteins and VLPs formation were detected by transmission electron microscopy (TEM) through colloidal gold immunolabeling and negative staining. Cell extracts containing recombinant proteins were purified by affinity chromatography and immunization of Balb/c mice with the formulation HPV16 L1/L2 VLPs containing adjuvant was able to induce higher titer of anti-HPV16 L1, when compared to HPV16 L2 antibodies by indirect ELISA assay. These data indicate that transient expression in 293-F cells was efficiently established. The results are promising for obtain recombinant proteins of the HPV capsid for future studies involving human papillomavirus, as well as to contribute for the development of other vaccine strategies for prevention against HPV.
High-human acuity of speed asymmetry during walking
Authors: Iturralde Pablo A. , Gonzalez-Rubio Marcela , Torres-Oviedo Gelsy
Published: October 2020

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Despite its central role in the proper functioning of the motor system, sensation has been less studied than motor output in sensorimotor adaptation paradigms. This deficit is probably due to the difficulty of measuring sensation: while motor output has easily observable consequences, sensation is by definition an internal variable of the motor system. In this study we asked how well can subjects estimate relevant environmental changes inducing motor adaptation. We addressed this question in the context of walking on a split-belt treadmill, which allows subjects to experience distinct belt speeds for each leg. We used a two-alternative forced-choice perceptual task (2AFC) in which subjects report which belt they thought to be moving slower. We characterized baseline accuracy in this task for healthy human subjects, and found 75% accuracy for 75 mm/s speed differences. Additionally, we used a drift-diffusion model of the task that could account for both accuracy and reaction times. We conclude that 2AFC tasks can be used to probe subjects’ estimates of the environment and that this approach opens an avenue for investigating perceptual deficits and its relation to motor impairments in clinical populations.
Apical PAR complex proteins protect against epithelial assaults to create a continuous and functional intestinal lumen
Authors: Sallee Maria D. , Pickett Melissa A. , Feldman Jessica L.
Published: October 2020

Sustained polarity and adhesion of epithelial cells is essential for the protection of our organs and bodies, and this epithelial integrity emerges during organ development amidst numerous morphogenetic assaults. Using the developingC. elegansintestine as anin vivomodel, we investigated how epithelial cells maintain integrity through cell division and elongation to build a functional tube. Live-imaging revealed that apical PAR complex proteins PAR-6/Par6 and PKC-3/aPkc remained apical during mitosis while apical microtubules and microtubule-organizing center (MTOC) proteins were transiently removed. Intestine-specific depletion of PAR-6, PKC-3, and the aPkc regulator CDC-42/Cdc42 caused persistent gaps in the apical MTOC as well as in other apical and junctional proteins after cell division and in non-dividing cells that elongated. Upon hatching, gaps coincided with luminal constrictions that blocked food, and larvae arrested and died. Thus, the apical PAR complex maintains apical and junctional continuity to construct a functional intestinal tube.