bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in Corneal Density After Accelerated Corneal Collagen Cross-linking With Different Irradiation Intensities and Energy Exposures: 1-Year Follow-up
Authors: Akkaya Turhan Semra , Toker Ebru
Published: September 2017

Purpose:

To determine and compare the changes in corneal density after 2 different protocols of accelerated corneal collagen cross-linking (A-CXL) in patients with progressive keratoconus.

Methods:

Two groups of eyes received A-CXL treatment; 20 eyes received A-CXL using continuous UVA light exposure at 9 mW/cm2 for 10 minutes with a total energy dose of 5.4 J/cm2, and 24 eyes received A-CXL using continuous UVA light exposure at 30 mW/cm2 for 4 minutes with a total energy dose of 7.2 J/cm2. Corneal density was measured with Scheimpflug tomography at 1, 3, 6, and 12 months of follow-up.

Results:

Densitometry peaked at 1 month (mean: 16.34 ± 3.80, P = 0.006, 9-mW/cm2 A-CXL; mean: 20.90 ± 2.81, P < 0.0001, 30-mw/cm2 A-CXL) in both groups, and it decreased over time in 30-mW/cm2 A-CXL. However, in 9-mW/cm2 A-CXL, increased corneal densitometry plateaued until 6 months postoperatively and started to decrease thereafter. Densitometry completely returned to baseline after 12 months in both groups. The mean change in density at 1- and 3-month follow-up was higher in the 30-mW A-CXL group than in the 9-mW A-CXL group (P = 0.003, P = 0.044; respectively).

Conclusions:

High-energy exposure tends to induce more haze in the early posttreatment period, but it is reversible.
Tear Osmolarity and Correlation With Ocular Surface Parameters in Patients With Dry Eye
Authors: Mathews Priya M. , Karakus Sezen , Agrawal Devika , Hindman Holly B. , Ramulu Pradeep Y. , Akpek Esen K.
Published: September 2017

Purpose:

To analyze the distribution of tear film osmolarity in patients with dry eye and its association with other ocular surface parameters.

Methods:

Tear osmolarity and other quantitative dry eye parameters were obtained from patients with 1) clinically significant dry eye (significant symptoms and ocular surface staining, n = 131), 2) symptoms-only dry eye (significant symptoms but no significant ocular surface staining, n = 52), and 3) controls (no significant symptoms or staining, n = 42).

Results:

Tear osmolarity varied significantly across groups (P = 0.01), with patients with clinically significant dry eye having the highest tear osmolarity (312.0 ± 16.9 mOsm/L), control patients having the lowest tear osmolarity (305.6 ± 9.7 mOsm/L), and patients with symptoms-only dry eye falling in between (307.4 ± 5.6 mOsm/L). Patients with clinically significant dry eye also tended to have a greater intereye difference in osmolarity (12.0 ± 13.4) than did the individuals with symptoms-only dry eye (9.1 ± 12.4) and controls (9.0 ± 7.4) (P = 0.06). In multivariable regression models, higher tear osmolarity was associated with higher Ocular Surface Disease Index, discomfort subscore (P = 0.02), and higher corneal and conjunctival staining scores (P < 0.01 for both). Worse eye tear osmolarity was not correlated with the corresponding tear film breakup time or Schirmer test (P > 0.05 for both).

Conclusions:

Individuals with symptomatic dry eye that is not yet clinically significant seem to have higher and more variable osmolarity measurements than controls, potentially indicating that changes in osmolarity precede clinical findings.
An Aesthetic Orbicularis Oculi Myectomy Technique for Blepharospasm: Use of Topical 5-Fluorouracil and Fibrin Sealant
Authors: Stewart Krista J. , Joseph Shannon S. , Douglas Raymond S.
Published: September 2017

Purpose:

To describe a modified technique of orbicularis oculi myectomy for refractory blepharospasm. This technique includes removal of orbicularis muscle, reformation of the eyelid crease and pretarsal platform using fibrin sealant (Tisseel), and topical 5-fluorouracil to reduce scar formation and improve aesthetic outcome.

Methods:

Retrospective chart review of 7 patients who underwent bilateral orbicularis oculi myectomy with our technique from 2013 to 2016. Outcome measures were postoperative botulinum toxin dose, frequency, duration between treatments, the amount of lagophthalmos, severity of dry eye, and patient satisfaction with aesthetic and functional outcome.

Results:

Patients who underwent the aesthetic myectomy technique had significantly decreased botulinum toxin use with relief of symptoms postoperatively. Only 1 of 7 patients experienced mild dry eye symptoms postoperatively, managed with artificial tears. All patients were satisfied with the aesthetic and functional outcome.

Conclusions:

The aesthetic myectomy technique provides effective treatment for blepharospasm with good functional and aesthetic outcome.
Extracorporeal Membrane Oxygenation for End-Stage Interstitial Lung Disease With Secondary Pulmonary Hypertension at Rest and Exercise: Insights From Simulation Modeling
Authors: Chicotka Scott , Burkhoff Daniel , Dickstein Marc L. , Bacchetta Matthew
Published: September 2017

Interstitial lung disease (ILD) represents a collection of lung disorders with a lethal trajectory with few therapeutic options with the exception of lung transplantation. Various extracorporeal membrane oxygenation (ECMO) configurations have been used for bridge to transplant (BTT), yet no optimal configuration has been clearly demonstrated. Using a cardiopulmonary simulation, we assessed different ECMO configurations for patients with end-stage ILD to assess the physiologic deficits and help guide the development of new long-term pulmonary support devices. A cardiopulmonary ECMO simulation was created, and changes in hemodynamics and blood gases were compared for different inflow and outflow anatomic locations and for different sweep gas and blood pump flow rates. The system simulated the physiologic response of patients with severe ILD at rest and during exercise with central ECMO, peripheral ECMO, and with no ECMO. The output parameters were total cardiac output (CO), mixed venous oxygen (O2) saturation, arterial pH, and O2 delivery (DO2)/O2 utilization (VO2) at different levels of exercise. The model described the physiologic state of progressive ILD and showed the relative effects of using various ECMO configurations to support them. It elucidated the optimal device configurations and required physiologic pump performance and provided insight into the physiologic demands of exercise in ILD patients. The simulation program was able to model the pathophysiologic state of progressive ILD with PH and demonstrate how mechanical support devices can be implemented to improve cardiopulmonary function at rest and during exercise. The information generated from simulation can be used to optimize ECMO configuration selection for BTT patients and provide design guidance for new devices to better meet the physiologic demands of exercise associated with normal activities of daily living.
Osteogenesis imperfecta: diagnosis and treatment
Authors: Palomo Telma , Vilaça Tatiane , Lazaretti-Castro Marise
Published: September 2017

Purpose of review

Here we summarize the diagnosis of osteogenesis imperfecta, discuss newly discovered genes involved in osteogenesis imperfecta, and review the management of this disease in children and adults.

Recent findings

Mutations in the two genes coding for collagen type I, COL1A1 and COL1A2, are the most common cause of osteogenesis imperfecta. In the past 10 years, defects in at least 17 other genes have been identified as responsible for osteogenesis imperfecta phenotypes, with either dominant or recessive transmission. Intravenous bisphosphonate infusions are the most widely used medical treatment. This has a marked effect on vertebra in growing children and can lead to vertebral reshaping after compression fractures. However, bisphosphonates are less effective for preventing long-bone fractures. At the moment, new therapies are under investigation.

Despite advances in the diagnosis and treatment of osteogenesis imperfecta, more research is needed. Bisphosphonate treatment decreases long-bone fracture rates, but such fractures are still frequent. New antiresorptive and anabolic agents are being investigated but efficacy and safety of these drugs, especially in children, need to be better established before they can be used in clinical practice.
Management of Acute Pancreatitis in the Pediatric Population
Authors: Abu‐El‐Haija Maisam , Kumar Soma , Quiros Jose Antonio , Balakrishnan Keshawadhana , Barth Bradley , Bitton Samuel , Eisses John F. , Foglio Elsie Jazmin , Fox Victor , Francis Denease , Freeman Alvin Jay , Gonska Tanja , Grover Amit S. , Husain Sohail Z. , Kumar Rakesh , Lapsia Sameer , Lin Tom , Liu Quin Y. , Maqbool Asim , Sellers Zachary M. , Szabo Flora , Uc Aliye , Werlin Steven L. , Morinville Veronique D.
Published: September 2017

Background:

Although the incidence of acute pancreatitis (AP) in children is increasing, management recommendations rely on adult published guidelines. Pediatric‐specific recommendations are needed.

Methods:

The North American Society for Pediatric Gastroenterology, Hepatology and Nutrition Pancreas committee performed a MEDLINE review using several preselected key terms relating to management considerations in adult and pediatric AP. The literature was summarized, quality of evidence reviewed, and statements of recommendations developed. The authorship met to discuss the evidence, statements, and voted on recommendations. A consensus of at least 75% was required to approve a recommendation.

Results:

The diagnosis of pediatric AP should follow the published INternational Study Group of Pediatric Pancreatitis: In Search for a CuRE definitions (by meeting at least 2 out of 3 criteria: (1) abdominal pain compatible with AP, (2) serum amylase and/or lipase values ≥3 times upper limits of normal, (3) imaging findings consistent with AP). Adequate fluid resuscitation with crystalloid appears key especially within the first 24 hours. Analgesia may include opioid medications when opioid‐sparing measures are inadequate. Pulmonary, cardiovascular, and renal status should be closely monitored particularly within the first 48 hours. Enteral nutrition should be started as early as tolerated, whether through oral, gastric, or jejunal route. Little evidence supports the use of prophylactic antibiotics, antioxidants, probiotics, and protease inhibitors. Esophago‐gastro‐duodenoscopy, endoscopic retrograde cholangiopancreatography, and endoscopic ultrasonography have limited roles in diagnosis and management. Children should be carefully followed for development of early or late complications and recurrent attacks of AP.

Conclusions:

This clinical report represents the first English‐language recommendations for the management of pediatric AP. Future aims should include prospective multicenter pediatric studies to further validate these recommendations and optimize care for children with AP.
Analysis of Tractor-Associated Fatalities
Authors: Türkoğlu Abdurrahim , Sehlikoğlu Kerem , Tokdemir Mehmet
Published: September 2017

Introduction and Objective

Tractor is regarded as a key equipment in agriculture, and it is also used for transportation and transfer purposes in addition to its agricultural use. Accidents resulting in death in farmlands are frequently encountered. Tractor-related fatalities are the most common ones among the deaths after farm accidents. This study aimed to evaluate the characteristics of tractor-related deaths and to discuss the measures that could be taken to prevent these deaths.

Methods

In this study, 42 cases who underwent postmortem examination and/or autopsy because of tractor fatalities in the province of Elazig between January 2005 and December 2016 were examined retrospectively with such variables as sex, age, month and season of incident, cause of incident, location of incident, position of case, and injured region.

Results

Of the cases, 36 (85.7%) were male, and 6 (14.3%) were female. The youngest case was 2 years old, and the oldest case was 83 years old; the mean age was 43.3 ± 25.0 years. Examining the deaths regarding the cause of incident showed that tractor rollover was the most common cause (42.9%). This was followed by being run over by the tractor (19.0%). Of the cases, 24 (57.1%) were drivers, 10 (23.8%) were passengers, and 8 (19.0%) were pedestrians.

Conclusions

Tractor-related fatalities due to tractor rollover are most often seen. To reduce the deaths caused by this reason, drivers should have special training and technical support, use helmets and seatbelts in the tractor, and have a health check at certain intervals (especially the drivers at advanced age).
A Histological Analysis of Visceral Organs to Evaluate the Effect of Duration of Heating From Refrigeration to Core Body Temperature for Ballistics Investigations
Authors: Humphrey Caitlin , Kumaratilake Jaliya
Published: September 2017

Animal organs have been used in ballistics research to investigate the effects on human organs. Such organs are refrigerated until the investigation to minimize autolytic degradation and at times have been reheated to the human core body temperature to simulate the in situ environment. The aim of this investigation was to study the microstructural changes that may occur in fresh chilled visceral organs of the thorax and abdomen (ie, heart, lung, liver, and kidney) during the period of reheating to 37°C. Fifty-millimeter cubes of porcine heart, lung, liver, and kidney were taken rapidly after slaughter, chilled overnight, and the next morning were reheated to core body temperature (37°C). Histological changes occurring in the tissues during the reheating phase were investigated. The findings indicated that no cytoplasmic or nuclear changes occurred in any of the tissues during the period of reheating. Therefore, reheating of animal organs to the human core body temperature is not necessary, if the organs are refrigerated.
Pediatric Mild Traumatic Brain Injury in the Acute Setting
Authors: Corwin Daniel J. , Grady Matthew F. , Joffe Mark D. , Zonfrillo Mark R.
Published: September 2017

Pediatric mild traumatic brain injuries, most of which are concussions, are an increasingly common reason for presentation to emergency departments. The diagnosis of concussion has increased dramatically over the past decade, necessitating the acute care provider to have up-to-date knowledge of the definition, pathophysiology, signs and symptoms, physical examination findings, and acute management of pediatric concussion. This article also addresses populations most vulnerable to prolonged recovery from pediatric concussion and referral recommendations.
The Association of Posttraumatic Stress Disorder With Clinic and Ambulatory Blood Pressure in Healthy Adults
Authors: Edmondson Donald , Sumner Jennifer A. , Kronish Ian M. , Burg Matthew M. , Oyesiku Linda , Schwartz Joseph E.
Published: September 2017

Objective

Posttraumatic stress disorder (PTSD) is associated with incident cardiovascular risk. We tested the association of PTSD with clinic and ambulatory blood pressure (ABP) in a sample of healthy participants and tested ABP reactivity to anxiety as a mechanism by which PTSD may influence blood pressure (BP).

Methods

Participants were originally enrolled during workplace BP screenings at three sites; approximately 6 years (standard deviation = 1.0) later, they completed nine clinic BP assessments within three visits, 1 week apart. Before the third visit, participants were screened for PTSD (≥33 on the PTSD Checklist–Civilian) and depression (Beck Depression Inventory) and then completed 24-hour ABP monitoring with electronic diary assessment of anxiety (0–100) at each awake reading.

Results

Of 440 participants, 92 (21%) screened positive for PTSD. In regression models adjusted for depression and demographic and clinical variables, PTSD was associated with greater mean systolic BP (3.8 mm Hg clinic [95% confidence interval {CI}] = 1.1–6.5,p= .006), 3.0 mm Hg awake ABP [95% CI = 0.1–5.9,p= .04], and a nonsignificant 2.1 mm Hg ABP during sleep [95% CI = −1.0 to 5.1,p= .18]). PTSD was associated with greater 24-hour median anxiety (p< .001), and changes in anxiety were positively associated with concurrent systolic ABP (p< .001). ABP reactivity to anxiety was greater in participants with PTSD, which partially explained the association of PTSD with ABP.

Conclusions

PTSD is associated with greater systolic BP, partly because of greater anxiety, and systolic BP reactivity to anxiety throughout the day. Daily anxiety and related BP reactivity may be targets for interventions to reduce the cardiovascular risk associated with PTSD.
Partner Loss in Monogamous Rodents: Modulation of Pain and Emotional Behavior in Male Prairie Voles
Authors: Osako Yoji , Nobuhara Reiko , Arai Young-Chang P. , Tanaka Kenjiro , Young Larry J. , Nishihara Makoto , Mitsui Shinichi , Yuri Kazunari
Published: September 2017

Objective

Pain is modulated by psychosocial factors, and social stress–induced hyperalgesia is a common clinical symptom in pain disorders. To provide a new animal model for studying social modulation of pain, we examined pain behaviors in monogamous prairie voles experiencing partner loss.

Methods

After cohabitation with novel females, males (n = 79) were divided into two groups on the basis of preference test scores. Half of the males of each group were separated from their partner (loss group), whereas the other half remained paired (paired group). Thus, males from both groups experienced social isolation. Open field tests, plantar tests, and formalin tests were then conducted on males to assess anxiety and pain-related behaviors.

Results

Loss males showing partner preferences (n = 20) displayed a significant increase in anxiety-related behavior in the open-field test (central area/total distance: 13.65% [1.58%] for paired versus 6.45% [0.87%] for loss; p < .001), a low threshold of thermal stimulus in the plantar test (withdrawal latencies: 9.69 [0.98] seconds for paired versus 6.15 [0.75] seconds for loss; p = .037), and exacerbated pain behaviors in the formalin test (total number of lifts: 40.33 [4.46] for paired versus 54.42 [1.91] for loss; p = .042) as compared with paired males (n = 20). Thermal thresholds in the plantar test significantly correlated with anxiety-related behavior in the open-field test (r = 0.64). No such differences were observed in the males that did not display partner preferences (r = 0.15).

Conclusions

Results indicate that social bonds and their disruption, but not social housing without bonding followed by isolation, modulate pain and emotion in male prairie voles. The prairie vole is a useful model for exploring the neural mechanisms by which social relationships contribute to pain and nociceptive processing in humans.
Soft Tissue Response on 18F-Fluorocholine PET/CT in Metastatic Castrate-Resistant Prostate Cancer Treated With 223Ra-Dichloride
Authors: Kwee Sandi A. , Lim John , Coel Marc N.
Published: September 2017

Two patients with castrate-resistant prostate cancer and symptomatic skeletal metastases underwent 18F-fluorocholine PET/CT prior to treatment with 223Ra-dichloride to reveal additional active lesions in the prostate gland and lymph nodes. Subsequent scans performed at the midpoint and end of 223Ra-dichloride therapy showed resolution of this soft tissue activity alongside declining bone lesion activity. Concomitant increases in plasma interleukin 6 were detected, suggesting that immune system activation may have mediated the soft tissue response. Abscopal effects usually encountered with external beam radiotherapy may also be occurring with 223Ra-dichloride therapy.
FDG PET/CT in 2 Cases of Renal Metastasis From Esophageal Squamous Cell Carcinoma
Authors: Zhao Qian , Dong Aisheng , Yang Bo , Wang Yang , Zuo Changjing
Published: September 2017

Clinically, renal metastasis from esophageal squamous cell carcinoma is uncommon. We present 2 cases of renal metastasis from esophageal squamous cell carcinoma with enhanced CT and FDG PET/CT findings. In the first case, right kidney and right renal hilum were the only known metastatic sites. In the second case, bilateral kidneys were the only known metastatic sites. All the renal metastatic tumors appeared as hypovascular and hypoattenuating masses involving both the renal cortex and medulla on enhanced CT and intense FDG uptake on FDG PET/CT.
89Zr-Trastuzumab PET/CT for Detection of Human Epidermal Growth Factor Receptor 2–Positive Metastases in Patients With Human Epidermal Growth Factor Receptor 2–Negative Primary Breast Cancer
Authors: Ulaner Gary A. , Hyman David M. , Lyashchenko Serge K. , Lewis Jason S. , Carrasquillo Jorge A.
Published: September 2017

Purpose

The aim of this study was to determine if imaging with 89Zr-trastuzumab, a human epidermal growth factor receptor 2 (HER2)–targeting PET tracer, can detect HER2-positive metastases in patients with HER2-negative primary breast cancer.

Methods

As part of an institutional review board–approved, prospective clinical trial of 89Zr-trastuzumab PET/CT (ClinicalTrials.gov identifier NCT02286843), a second group of 11 patients with HER2-negative primary breast cancer and known metastatic disease were recruited. Patients with confirmed HER2-negative primary breast cancer underwent 89Zr-trastuzumab PET/CT to screen for 89Zr-trastuzumab–avid lesions suggestive of unsuspected HER2-positive metastases. 89Zr-trastuzumab–avid lesions on PET/CT were biopsied and pathologically examined to determine HER2 status.

Results

All 11 patients had confirmed HER2-negative primary breast cancer. Four patients demonstrated suspicious foci on 89Zr-trastuzumab PET/CT. Of these 4 patients, 1 patient had biopsy-proven HER2-positive metastases. The other 3 patients with suspicious 89Zr-trastuzumab–avid foci had biopsy demonstrating a metastasis that was HER2-negative and were considered false-positive 89Zr-trastuzumab PET foci. Combined with a published report of the first 9 patients, there have been a total of 20 HER2-negative primary breast cancer patients, with 3 patients (15%) having pathologically confirmed HER2-positive distant metastases and 6 (30%) with suspicious 89Zr-trastuzumab–avid foci that were HER2-negative on pathology, which were thus considered false-positive 89Zr-trastuzumab findings.

Conclusions

This second group of patients confirms the proof of concept that 89Zr-trastuzumab PET/CT detects unsuspected HER2-positive metastases in a subset of patients with HER2-negtive primary breast cancer. False-positive 89Zr-trastuzumab–avid foci present a challenge to using this tracer.
Methionine PET Might Be Reliable for the Detection of Low M-Protein–Producing Myelomas
Authors: Imataki Osamu , Uchida Shumpei , Yokokura Shigeyuki , Uemura Makiko , Kadowaki Norimitsu
Published: September 2017

11C-methionine (MET) positron emission tomography (PET) is more sensitive than 18F-fluorodeoxyglucose (FDG)–PET for detecting myeloma lesion. Many clinical studies support this evidence mainly for multiple myeloma cases of IgG or IgA subtypes. However, this is not confirmed for low monoclonal protein-producing myelomas, such as IgD, IgE, and nonsecretory type. We encountered a 71-year-old man with IgD λ-type myeloma. In this patient, FDG-PET did not reveal any abnormal uptake lesions, whereas MET-PET revealed diffuse bone marrow uptake that relieved after initial chemotherapy. We speculate that the determinants for high serological activity of protein metabolism are transporter system activity or proliferation index.
Advantages of a Beveled Osteotomy on the Zygomatic Arch During Reduction Malarplasty
Authors: Lee Tae Sung , Park Sanghoon
Published: September 2017

During a conventional reduction malarplasty procedure, a dual approach including intraoral incisions and preauricular incisions is made to reduce both the zygomatic body and arch. As the preauricular approach is performed to cut the zygomatic arch, there are several remarkable advantages that can be achieved by simply beveling the osteotomy anteriorly on the zygomatic arch. This has the benefits of enhancing bone union by the increase in cross-sectional area for bone contact, decreasing palpability on the osteotomy site, placing the osteotomy more posteriorly, preventing depression in the anterior malar region, and reducing the need for metal fixtures.
A Rare Cause of Dyspnea: Cervicothoracic Cystic Lymphangioma
Authors: Jo Min Seop , Jeong Jin Yong
Published: September 2017

I read with great interest the article reported by Efe et al in Journal of Cranofacial Surgery (2016;27:1802-1803), presenting the excellent result obtained by the use of sclerotherapy with single-dose OK-432 in a growing cervical lymphangioma. Cervicothoracic lymphangioma is a rare congenital anomaly that is mostly asymptomatic. We would like to share our experience of a rare cause of dyspnea by lymphangioma. In our case, the patient presented with dyspnea and paroxysmal cough caused by cervicothoracic lymphangioma and sclerotherapy alleviated tracheal compression and relieved the dyspneic symptoms.
Massive Intradural Dermoid Cyst Without Sinus Tract
Authors: Abouhassan William , Chao John An Kuang , Lehman James A.
Published: September 2017

Dermoid cysts can present as a rare, benign, congenital intracranial tumor of neuroectoderm origin trapped during embryogenesis. Past clinical reports have reported lesions in the posterior fossa, at the midline, and in the intradural region all in conjunction with a superficial sinus tract. The authors present a unique patient of a completely intracranial, intradural, dermoid tumor of the midline cerebellum devoid of any evidence of sinus tract. The histological characteristics, radiological features, and management of this unusual patient are described.
Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility
Authors: Grotjahn Danielle A. , Chowdhury Saikat , Xu Yiru , McKenney Richard J. , Schroer Trina A. , Lander Gabriel C.
Published: September 2017

A key player in the intracellular trafficking network is cytoplasmic dynein, a protein complex that transports molecular cargo along microtubule tracks. It has been shown that vertebrate dynein’s movement becomes strikingly enhanced upon interacting with a cofactor named dynactin and one of several cargo-adapters, such as BicaudalD2. However, the mechanisms responsible for this increase in transport efficiency are not well understood, largely due to a lack of structural information. We used cryo-electron tomography to visualize the first 3-dimensional structure of the intact dynein-dynactin complex bound to microtubules. Our structure reveals that the dynactin-cargo-adapter complex recruits and binds to two dimeric cytoplasmic dyneins. Interestingly, the dynein motor organization closely resembles that of axonemal dynein, suggesting that cytoplasmic dynein and axonemal dyneins may utilize similar mechanisms to coordinate multiple motors. We propose that grouping dyneins onto a single dynactin scaffold promotes collective force production as well as unidirectional processive motility. These findings provide a structural platform that facilitates a deeper biochemical and biophysical understanding of dynein regulation and cellular transport.
Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity
Authors: Constance William D , Mukherjee Amrita , Fisher Yvette E , Pop Sînziana , Blanc Eric , Toyama Yusuke , Williams Darren W
Published: September 2017

Building arborisations of the right size and shape is fundamental for neural network function. Live imaging studies in vertebrate brains strongly suggest that nascent synapses are critical for branch growth during the development of axonal and dendritic arborisations. The molecular mechanisms underlying such ‘synaptotropic’ events are largely unknown.

Here we present a novel system inDrosophilafor studying the development of complex axonal arborisations live,in vivoduring metamorphosis. In these growing axonal arborisations we see a relationship between the punctate localisations of presynaptic components and branch dynamics that is very similar to synaptotropic growth described in fish and frogs. These presynaptic components however do not appear to represent functional presynaptic release sites and are not paired with clusters of neurotransmitter receptors. Pharmacological and genetic knockdowns of evoked and spontaneous neurotransmission do not impact the outgrowth of these neurons. Instead, we find that axonal branch growth is regulated by the dynamic focal localisations of synaptic adhesion proteins Neurexin and Neuroligin. These adhesion complexes provide selective stability for filopodia by a ‘stick and grow’-based mechanism wholly independent of synaptic activity.
Minor spliceosome inactivation in the developing mouse cortex causes self-amplifying radial glial cell death and microcephaly
Authors: Baumgartner Marybeth , Olthof Anouk M. , Hyatt Katery C. , Lemoine Christopher , Drake Kyle , Sturrock Nikita , Nguyen Nhut , Al Seesi Sahar , Kanadia Rahul N.
Published: September 2017

Inactivation of the minor spliceosome has been linked tomicrocephalicosteodysplasticprimordialdwarfism type1(MOPD1). To interrogate how minor intron splicing regulates cortical development, we employedEmx1-Cre to ablateRnu11, which encodes the minor spliceosome-specific U11 small nuclear RNA (snRNA), in the developing cortex (pallium).Rnu11cKO mice were born with microcephaly, caused by death of self-amplifying radial glial cells (RGCs). However, both intermediate progenitor cells (IPCs) and neurons were produced in the U11-null pallium. RNAseq of the pallium revealed elevatedminor intron retention in the mutant, particularly in genes regulating cell cycle. Moreover, the only downregulated minor intron-containing gene (MIG) wasSpc24, which regulates kinetochore assembly. These findings were consistent with the observation of fewer RGCs entering cytokinesis prior to RGC loss, underscoring the requirement of minor splicing for cell cycle progression in RGCs. Overall, we provide a potential explanation of how disruption of minor splicing might cause microcephaly in MOPD1.

Summary Statement

Here we report the first mammalian model to investigate the role of the minor spliceosome in cortical development and microcephaly.

List of abbreviations used

MOPD1=microcephalic osteodysplastic primordial dwarfism type 1; snRNA=small nuclear RNA; cKO=conditional knockout; NPC=neural progenitor cell; RGC=radial glial cell; IPC=intermediate progenitor cell; MIG=minor intron-containing gene
SpliceVec: distributed feature representations for splice junction prediction
Authors: Dutta Aparajita , Dubey Tushar , Singh Kusum Kumari , Anand Ashish
Published: September 2017

Identification of intron boundaries, called splice junctions, is an important part of delineating gene structure and functions. This also provides valuable in-sights into the role of alternative splicing in increasing functional diversity of genes. Identification of splice junctions through RNA-seq is by mapping short reads to the reference genome which is prone to errors due to random sequence matches. This encourages identification of splicing junctions through computa-tional methods based on machine learning. Existing models are dependent on feature extraction and selection for capturing splicing signals lying in vicinity of splice junctions. But such manually extracted features are not exhaustive. We introduce distributed feature representation,SpliceVec, to avoid explicit and biased feature extraction generally adopted for such tasks. SpliceVec is based on two widely used distributed representation models in natural language processing. Learned feature representation in form of SpliceVec is fed to multi-layer perceptron for splice junction classification task. An intrinsic evaluation of SpliceVec indicates that it is able to group true and false sites distinctly. Our study on optimal context to be considered for feature extraction indicates inclusion of entire intronic sequence to be better than flanking upstream and downstream region around splice junctions. Further, SpliceVec is invariant to canonical and non-canonical splice junction detection. The proposed model is consistent in its performance even with reduced dataset and class-imbalanced dataset. SpliceVec is computationally efficient and can be trained with user defined data as well.
Alterations in neurovascular coupling following acute traumatic brain injury
Authors: Jang Hyounguk , Huang Stanley , Hammer Daniel X. , Wang Lin , Ye Meijun , Welle Cristin G. , Fisher Jonathan A. N.
Published: September 2017

Traumatic brain injury (TBI) is a leading cause of mortality and disability worldwide. A challenge for diagnosing and assessing the severity of TBI, however, is that quantitative biomarkers are lacking. We explored potential functional indicators for TBI by noninvasively monitoring sensory-evoked electrical and hemodynamic activity using a novel hybrid optical and electrophysiological measurement approach. By combining diffuse correlation spectroscopy with co-localized electrophysiological measurements in a mouse model of TBI, we observed concomitant alterations in somatosensory-evoked cerebral blood flow and electrical potentials following controlled cortical impact. Injury acutely reduced the amplitude of stimulus-evoked responses, which mostly recovered to baseline values within 30 min; intertrial variability for these parameters was also acutely altered. The kinetics of recovery, however, varied among specific components of the evoked waveforms, and we observed strong correlations between the two measurement modalities for only a select subset of waveform parameters. Overall, our results identify a novel set of potential biomarkers for TBI and demonstrate the utility of combined, noninvasive optical and electrophysiological measurements for detecting injury-induced abnormalities in neurovascular reactivity.
Cryo-EM shows how dynactin recruits two dyneins for faster movement
Authors: Urnavicius Linas , Lau Clinton K. , Elshenawy Mohamed M. , Morales-Rios Edgar , Motz Carina , Yildiz Ahmet , Carter Andrew P.
Published: September 2017

Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein/dynactin to distinct cargos. Here we use electron microscopy (EM) and single molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased toward recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two. We find that the shift toward a double dynein complex increases both force and speed. A 3.5 Å cryo-EM reconstruction of a dynein tail/dynactin/BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side by side. Our work provides a structural basis for how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein/dynactin transport machine.
A minimal model of protein allocation during phototrophic growth
Authors: Faizi Marjan , Zavřel Tomáš , Loureiro Cristina , Cerveny Jan , Steuer Ralf
Published: September 2017

Photoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function, typically reduces the proteome available for other cellular functions. Here, we develop a minimal semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation. The model is parametrized using literature data and experimentally obtained growth curves. Of particular interest are the resulting cyanobacterial growth laws as fundamental characteristics of cellular growth. We show that the model gives rise to similar growth laws as observed for heterotrophic organisms, with several important differences due to the distinction between light energy and carbon uptake. We discuss recent experimental data supporting the model results and show that minimal growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.
The actin cytoskeleton governs apical mitosis and daughter cell dispersion in intestinal epithelia
Authors: McKinley Kara L. , Stuurman Nico , Klein Ophir D. , Vale Ronald D.
Published: September 2017

Cell proliferation is critical for maintaining the absorptive, protective and regenerative functions of the small intestine throughout adulthood. Interphase nuclei are positioned near the basal surface of the intestinal epithelium, but during mitosis, chromosomes are located apically. The molecular basis for apical-basal DNA positioning and its consequences for tissue homeostasis are poorly understood. Here, we image and pharmacologically perturb these behaviors in live murine intestinal organoids. We find that apical and basal DNA movements occur as a result of mitosis-coupled actin rearrangements that alter the basolateral shape of dividing cells, while the apical cell surface remains confined by cell-cell contacts that persist throughout mitosis. Strikingly, these polarized shape changes allow neighboring cells to insert between nascent daughters, intermingling cells of different lineages. In summary, polarized rearrangements of the actin cytoskeleton govern the mitotic behavior of intestinal epithelial cells and lead to interspersion of cell lineages.
Reprogramming human T cell function and specificity with non-viral genome targeting
Authors: Roth Theodore L. , Puig-Saus Cristina , Yu Ruby , Shifrut Eric , Carnevale Julia , Hiatt Joseph , Saco Justin , Li Han , Li Jonathan , Tobin Victoria , Nguyen David , Ferris Andrea M. , Chen Jeff , Schickel Jean-Nicolas , Pellerin Laurence , Carmody David , Alkorta-Aranburu Gorka , Del Gaudio Daniela , Matsumoto Hiroyuki , Morell Montse , Mao Ying , Quadros Rolen , Gurumurthy Channabasavaiah , Smith Baz , Haugwitz Michael , Hughes Stephen H. , Weissman Jonathan , Schumann Kathrin , May Andrew P. , Ashworth Alan , Kupfer Gary , Greeley Siri , Bacchetta Rosa , Meffre Eric , Roncarolo Maria Grazia , Romberg Neil , Herold Kevan C. , Ribas Antoni , Leonetti Manuel D. , Marson Alexander
Published: September 2017

Human T cells are central to physiological immune homeostasis, which protects us from pathogens without collateral autoimmune inflammation. They are also the main effectors in most current cancer immunotherapy strategies1. Several decades of work have aimed to genetically reprogram T cells for therapeutic purposes2–5, but as human T cells are resistant to most standard methods of large DNA insertion these approaches have relied on recombinant viral vectors, which do not target transgenes to specific genomic sites6, 7. In addition, the need for viral vectors has slowed down research and clinical use as their manufacturing and testing is lengthy and expensive. Genome editing brought the promise of specific and efficient insertion of large transgenes into target cells through homology-directed repair (HDR), but to date in human T cells this still requires viral transduction8, 9. Here, we developed a non-viral, CRISPR-Cas9 genome targeting system that permits the rapid and efficient insertion of individual or multiplexed large (>1 kilobase) DNA sequences at specific sites in the genomes of primary human T cells while preserving cell viability and function. We successfully tested the potential therapeutic use of this approach in two settings. First, we corrected a pathogenicIL2RAmutation in primary T cells from multiple family members with monogenic autoimmune disease and demonstrated enhanced signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR redirecting T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized the tumour antigen, with concomitant cytokine release and tumour cell killing. Taken together, these studies provide preclinical evidence that non-viral genome targeting will enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells.
Functional traits and community composition: multilevel models outperform community-weighted means
Authors: Miller Jesse E. D. , Damschen Ellen I. , Ives Anthony R.
Published: September 2017

Plant functional traits are increasingly being used to infer mechanisms about community assembly and predict global change impacts. Of the several approaches that are used to analyze trait-environment relationships, one of the most popular is community-weighted means (CWM), in which species trait values are averaged at the site level. Other approaches that do not require averaging are being developed, including multilevel models (MLM, also called generalized linear mixed models). However, relative strengths and weaknesses of these methods have not been extensively compared.

We investigated three statistical models for trait-environment associations: CWM, a MLM in which traits were not included as fixed effects (MLM1), and a MLM with traits as fixed effects (MLM2). We analyzed a real plant community dataset to investigate associations between two traits and one environmental variable. We then analyzed permutations of the dataset to investigate sources of type I errors, and performed a simulation study to compare the statistical power of the methods.

In the analysis of real data, CWM gave highly significant associations for both traits, while MLM1 and MLM2 did not. UsingP-values derived by simulating the data using the fitted MLM2, none of the models gave significant associations, showing that CWM had inflated type I errors (false positives). In the permutation tests, MLM2 performed the best of the three approaches. MLM2 still had inflated type I error rates in some situations, but this could be corrected using bootstrapping. The simulation study showed that MLM2 always had as good or better power than CWM. These simulations also confirmed the causes of type I errors from the permutation study.

The MLM that includes main effects of traits (MLM2) is the best method for identifying trait-environmental association in community assembly, with better type I error control and greater power. Analyses that regress CWMs on continuous environmental variables are not reliable because they are likely to produce type I errors.
Live Imaging of Chromosome Segregation during Meiosis in the Fission Yeast Schizosaccharomyces pombe
Authors: Yamashita Akira , Sakuno Takeshi , Watanabe Yoshinori , Yamamoto Masayuki
Published: September 2017

This protocol describes the live observation of chromosome segregation during fission yeast meiosis. To visualize one chromosome of interest, the lac operator (lacO array) is integrated at its centromere-proximal locus, and the lac repressor (lacI)-GFP fusion protein is expressed in a haploid strain. This haploid strain, in which mCherry-tagged tubulin is also expressed exogenously to monitor meiotic progression, is crossed with a nonlabeled haploid strain to induce meiosis. GFP and mCherry signals in resulting zygotes are observed by a fluorescent microscopy during the progression of meiosis.
Modification of Antibody Function by Mutagenesis
Authors: Dasch James R. , Dasch Amy L.
Published: September 2017

The ability to “fine-tune” recombinant antibodies by mutagenesis separates recombinant antibodies from hybridoma-derived antibodies because the latter are locked with respect to their properties. Recombinant antibodies can be modified to suit the application: Changes in isotype, format (e.g., scFv, Fab, bispecific antibodies), and specificity can be made once the heavy- and light-chain sequences are available. After immunoglobulin heavy and light chains for a particular antibody have been cloned, the binding site—namely, the complementarity determining regions (CDR)—can be manipulated by mutagenesis to obtain antibody variants with improved properties. The method described here is relatively simple, uses commercially available reagents, and is effective. Using the pComb3H vector, a commercial mutagenesis kit, PfuTurbo polymerase (Agilent), and two mutagenic primers, a library of phage with mutagenized heavy and light CDR3 can be obtained.
Injecting Embryonic Stem Cells into Eight-Cell-Stage Mouse Embryos
Authors: Auerbach Wojtek , DeChiara Thomas M.
Published: September 2017

In this protocol, eight-cell-stage precompaction embryos from outbred mouse strains are used for the injection of hybrid or inbred embryonic stem (ES) cells. This process often leads to generation of fully ES cell-derived so-called F0 mice (VelociMice). Postinjection culture of embryos is necessary to achieve the highest ratio of fully ES cell-derived mice and high-degree chimeras. Typically, 50 embryos are injected per ES cell clone.
Metabolomics in Yeast
Authors: Caudy Amy A. , Mülleder Michael , Ralser Markus
Published: September 2017

Budding yeast has from the beginning been a major eukaryotic model for the study of metabolic network structure and function. This is attributable to both its genetic and biochemical capacities and its role as a workhorse in food production and biotechnology. New inventions in analytical technologies allow accurate, simultaneous detection and quantification of metabolites, and a series of recent findings have placed the metabolic network at center stage in the physiology of the cell. For example, metabolism might have facilitated the origin of life, and in modern organisms it not only provides nutrients to the cell but also serves as a buffer to changes in the cellular environment, a regulator of cellular processes, and a requirement for cell growth. These findings have triggered a rapid and massive renaissance in this important field. Here, we provide an introduction to analysis of metabolomics in yeast.
Eco-efficiency measurement and improvement of Chinese industry using a new closest target method
Authors: Xiong Beibei , Li Yongli , Santibanez Gonzalez Ernesto D.R. , Song Malin
Published: September 2017

Purpose

The purpose of this paper is to measure Chinese industries’ eco-efficiency during 2006-2013. The Chinese industry attained rapid achievement in recent decades, but meanwhile, overconsumption of energy and environmental pollution have become serious problems. To solve these problems, many research studies used the data envelopment analysis (DEA) to measure the Chinese industry’s eco-efficiency. However, because the target set by these works is usually the furthest one for a province to be efficient, it may hardly be accepted by any province.

Design/methodology/approach

This paper builds a new “closest target method” based on an additive DEA model considering the undesirable outputs. This method is a mixed-integer programming problem which can measure the ecological efficiency of provinces and more importantly guide the province to perform efficiently with minimum effort.

Findings

The results show that the eco-efficiency of Chinese provinces increased at the average level, but the deviations remained at a larger value. Compared to the “furthest” target methods, the targets by the approach proposed by this study are more acceptable for a province to improve its performance on both economy and environment counts.

Originality/value

This study is the first attempt to introduce the closest targets concept to measure the eco-efficiency and set the target for each provincial industry in China.