bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of Scanning Acoustic Microscopy for Micro Delamination Detection
Authors: Kim Hyunsoo , Lee Seunghyuck , Kim Hakbeom , Kim Sanga
Published: December 2020

This paper describes the detection capability of micro delamination in ICs according to the transducer frequency of SAM (Scanning Acoustic Microscopy) equipment through a case study of non-destructive failure analysis. The analysis of scanning acoustic microscopy is non-destructive, but is difficult to define micro de-lamination or micro crack. In this study, two SAM systems and various transducer frequencies were used to detect micro de-lamination on the lead finger area. In the results of non-destructive analysis by utilizing two systems, one SAM detected the micro delamination but the other SAM did not define micro delamination with C-scan mode. To confirm an accurate delamination phenomenon, we analyze the destructive analysis under cross-sectional inspection and the micro de-lamination was observed. The cause of non-detection for micro delamination is not due to the difference between equipments, but due to the transducer frequency. This paper will be concluded with a discussion on what kind of transducer frequency are selected according to distance from package surface to chip surface, package materials, and micro de-lamination thickness.
Method of Recovering SEM Inspection Induced MOSFETs Degradation before Electrical Characterization
Authors: Lin Qi , Pan Hans , Chang Jonathan , Lin Rung-Jiun , Chang Shih-Hsin , Kuo Pau-Sheng , Chu Chih-Hsun
Published: December 2020

With technology scaling, semiconductor devices have become more prone to damage induced by SEM inspection. In this work, we find that today’s widely-used 0.5KeV SEM can also alter the electrical performance of the devices at 20nm technology node. Vts shift with SEM exposure time on nMOS and pMOS has been studied extensively. The cause of the degradation is the positive charge trapped in the gate oxide during SEM radiation. A conventional UV_eraser for EPROM was applied to SEM-damaged devices. The measurement data show that UV exposure can cure most of SEM-induced damage. In the future, if a regular SEM inspection is followed by nanoprobing device characterization, UV curing or another curing methods is required to recover the electric characteristics of the device before nanoprobing.
Multiphoton OBIC for Device Characterization and Defect Localization
Authors: Johnson Gregory M. , Smith Lloyd , Xu Ziyan , Nakamura Tomonori
Published: December 2020

Applications of MpOBIC (Multi-photon Optical Beam Induced Current) are discussed for use in defect localization. The MpOBIC signals in a ring oscillator under static conditions are examined and demonstrate the superior optical resolution of the system over traditional OBIRCH. A 5-fin diode test structure is examined under passive conditions, demonstrating that true multi-photon OBIC has occurred from the backside. The same diode is examined in forward bias, and the resulting discussion concludes that both OBIC and OBIRCH signals are present in the sample. Thus, we claim that both OBIC and OBIRCH signals can provide device characterization information from an MpOBIC system.
Investigation of Radiation-Induced Response in Advanced Microprocessor
Authors: Bossev Dobrin P. , Duncan Adam R. , Gadlage Matthew J. , Roach Austin H. , Kay Matthew J. , Berger Tammy J. , York Darin A. , Williams Aaron , Ingalls James D. , Szabo Carl M. , LaBel Kenneth A.
Published: December 2020

This work investigates the origin of the single event hard failures of an advanced commercial FinFET microprocessor induced by heavy ions using a combination of failure analysis tools. It focuses on elucidating the reason behind the hard and catastrophic failures of Intel 5th Generation MCP Broadwell microprocessors due to exposure to ionizing radiation. The failure analysis techniques point toward the same area on the platform control hub (PCH) die. Contrary to the initial (intuitive) hypothesis, the hard failures observed in the Intel 5th Generation MCP Broadwell are caused by 32-nm planar PCH die. These failures do not seem to be anyhow related to the FinFET technology, but the exact physical mechanism has yet to be identified. In conclusion, no critical issues or showstoppers were observed during heavy ion testing of Intel 14-nm Tri-Gate FinFET commercial microprocessors, which would prevent these devices from being considered as future space candidate parts.
Optimizing Ex-Situ Lift Out for Frontside or Backside FIB Milling
Authors: Giannuzzi Lucille A.
Published: December 2020

Ex situ lift out is fast, easy, and reproducible, and adds flexibility for either frontside or backside manipulation of focused ion beam milled specimens. ex situ lift out methods may be enhanced by eliminating electrostatic forces. In addition, optimizing the geometry of the specimen relative to the probe improves the Van der Waals forces responsible for the lift out and subsequent manipulation of focused ion beam prepared specimens.
Steps Toward Automated Deprocessing of Integrated Circuits
Authors: Principe E.L. , Asadizanjani Navid , Forte Domenic , Tehranipoor Mark , Chivas Robert , DiBattista Michael , Silverman Scott , Marsh Mike , Piche Nicolas , Mastovich John
Published: December 2020

This paper discusses the development of an extensible programmatic workflow that leverages evolving technologies in 2D/3D imaging, distributed instrument control, image processing, and automated mechanical/chemical deprocessing technology. Initial studies involve automated backside mechanical ultra-thinning of 65nm node IC processor chips in combination with SEM imaging and X-ray tomography. Areas as large as 800μm x 800μm were deprocessed using gas-assisted plasma FIB delayering. Ongoing work involves enhancing the workflow with “intelligent automation” by bridging FIB-SEM instrument control and near real-time data analysis to establish a computationally guided microscopy suite.
Maximizing the Electron Microscopy Contrasts for Analysis
Authors: Toh Suey Li , Ji Rong
Published: December 2020

To characterize materials or devices in the next generation cutting-edge technologies, it is becoming more essential to carry out comprehensive characterization of the samples with a system that can provide a wealth of various contrast information. By analyzing the different signals detected at different angular scattering distribution, it can reveal tremendous information from the samples. Coupled with the superior detection capability, we have demonstrated the capability to enhance the fault isolation methodology of memory devices or media grain size analysis by optimizing various parameter settings. The effects of conditions (accelerating voltage, working distance, detector, probe current etc.) that can influence the trajectory pathways or yield of the different emitted signals would be discussed in the paper.
In-Line Electron Beam Inspection of High Aspect-Ratio RMG FINFET Gate
Authors: Hafer Richard F. , Patterson Oliver D. , Gow Cathy , McKindles Derek , Hsieh Brian Yueh-Ling , Tang Xiaohu
Published: December 2020

For a recent replacement metal gate (RMG) technology using a SOI substrate, residue from the dummy gate formed a defect that affected the RMG formation. In this FINFET technology, the high aspect ratio of the gate makes removing the dummy gate very difficult. Residue is left behind, especially in multi-fin structures. This residue was poorly detected by existing Broad-Band-Plasma inspection and thus required Electron Beam Inspection. However, this physical inspection is challenging due to high aspect ratio of the gate and an insulating wafer surface. The defect was verified using TEM, and careful sample prep is shown to be critical to verify the defect. The high aspect ratio and insulating sample in a charged-particle inspection is investigated with Monte-Carlo (MC) simulations.
Techniques in Extracting CSP Device from Underfilled PCB Module and Performing Solder Rework and Reballing for ATE Testing
Authors: Cheong Kah Chin
Published: December 2020

The application of underfill materials for board level assembly has been increasing rapidly in semiconductor industry to enhance strength and reliability performance of semiconductor components in harsh environments. However, due to the intractability of the capillary underfill after curing, extracting a chip scale package (CSP) device from a printed circuit board (PCB) with a combination of mold compound and capillary underfill for ATE testing has become difficult and challenging. This poses a severe limitation to this technology regarding electrical testing and failure analysis. In order to address the challenge in extracting a CSP device from an underfilled PCB without inducing any mechanical damage, a series of sample preparation techniques has been introduced. This paper discusses the techniques in removing the fine pitch CSP device from underfilled PCB module in a relatively simple way which includes application of chemical solutions, de-soldering, residual solder remnants cleaning and reballing. The established process enables ATE testing, electrical testing and failure analysis to be performed on any CSP devices. An electrical evaluation on the efficiency of a CSP device after a series of sample preparation processes will also be highlighted.
Improved Phase Data Acquisition for Thermal Emissions Analysis of 2.5D IC
Authors: Zee Bernice , Qiu Wen , Foo Fangjie , Lai Brian , Vickers Jim , Tien David
Published: December 2020

Lock-in thermography (LIT) phase data is used to generate phase shift versus applied lock-in frequency plots to estimate defect depth in semiconductor packages. Typically, samples need to be tested for an extended time to ensure data consistency. Furthermore, determining the specific point on the thermal emission site to collect data from can be challenging, especially if it is large and dispersive. This paper describes how the use of new computational algorithms along with streamlined and automated workflows, such as self-adjusting thermal emission site positioning and phase measurement auto-stop, can result in improvements to data repeatability and accuracy as well as faster time to results. The new software is applied to generate the empirical phase shift versus applied lock-in frequency plot using 2.5D IC devices with known defect location. Subsequently, experimental phase shift data from reject 2.5D IC devices with unknown defect locations are obtained and compared against the empirical phase shift plot. The defect Z-depth of these devices are determined by comparing where the experimental phase shift data points lies with respect to empirical phase shift plot and validated with physical failure analysis (PFA).
Pattern Matching Rule Ranking Through Design of Experiments and Silicon Validation
Authors: Rajavendra Reddy Gaurav , Wallner Jin , Babich Katherina , Makris Yiorgos
Published: December 2020

Continued technology scaling has led to exposure of many ‘weak-points’ in the designs fabricated in some of the most advanced technology nodes. Weak-points are certain layout patterns which are found to be sensitive to process non-idealities and have a higher tendency to cause defects. They may be coded in the form of Pattern Matching (PM) rules and included within the Design for Manufacturability Guidelines (DFMGs) to ensure product manufacturability. Often, during Integrated Circuit (IC) design, a trade-off is made between meeting performance specifications and complying with DFMGs. As a result, designs may reach the foundry with some DFMG violations. Fixing such violations generally causes a ‘ripple effect’ where one change requires many changes in other metal layers, making the process tedious. Therefore, providing a ranked list of guidelines to the designers helps them in assessing the criticality of violations, prioritizing, and fixing them accordingly. Past research suggests using diagnosis data to determine the impact of DFMG violations. However, this is a reactive approach wherein DFMGs are ranked only based on their hard-defect causing nature. To make the ranking process more robust, we propose a proactive silicon validation based approach which not only considers the yield loss due to hard-defects but also takes into account the parametric and reliability degradation caused by DFMG violations. We evaluate the effectiveness of the proposed methodology through on-silicon experiments on an advanced Fully-Depleted Silicon-On-Insulator (FD-SOI) technology node.
WLCSP Laminate Removal Using NIR Laser
Authors: Khoo Chun Haur
Published: December 2020

Driven by the cost reduction and miniaturization, Wafer Level Chip Scale Packaging (WLCSP) has experienced significant growth mainly driven by mobile consumer products. Depending on the customers or manufacturing needs, the bare silicon backside of the WLCSP may be covered with a backside laminate layer. In the failure analysis lab, in order to perform the die level backside fault isolation technique using Photon Emission Microscope (PEM) or Laser Signal Injection Microscope (LSIM), the backside laminate layer needs to be removed. Most of the time, this is done using the mechanical polishing method. This paper outlines the backside laminate removal method of WLCSP using a near infrared (NIR) laser that produces laser energy in the 1,064 nm range. This method significantly reduces the sample preparation time and also reduces the risk of mechanical damage as there is no application of mechanical force. This is an effective method for WLCSP mounted on a PCB board.
Quantitative Imaging of Carrier Distribution in Silicon Solar Cell Using Scanning Nonlinear Dielectric Microscopy
Authors: Hirose Kotaro , Cho Yasuo , Tanahashi Katsuto , Takato Hidetaka
Published: December 2020

The carrier distribution in solar cell is important evaluation target. Scanning nonlinear dielectric microscopy is applied to the cross section of phosphorus implanted emitter in monocrystalline silicon solar cell and visualizes the carrier distribution quantitatively. The effective diffusivities of phosphorus are estimated from the experimental results. Then, the three-dimensional carrier distribution is simulated. The experimental and simulation results show good correlation.
Nanoprobe Characterization of Soft SRAM bit Fails in Advanced Technologies
Authors: Kodali Satish , Zhe Chen , Khiam Oh Chong
Published: December 2020

Nanoprobing is one of the key characterization techniques for soft defect localization in SRAM. DC transistor performance metrics could be used to identify the root cause of the fail mode. One such case report where nanoprobing was applied to a wafer impacted by significant SRAM yield loss is presented in this paper where standard FIB cross-section on hard fail sites and top down delayered inspection did not reveal any obvious defects. The authors performed nanoprobing DC characterization measurements followed by capacitance-voltage (CV) measurements. Two probe CV measurement was then performed between the gate and drain of the device with source and bulk floating. The authors identified valuable process marginality at the gate to lightly doped drain overlap region. Physical characterization on an inline split wafer identified residual deposits on the BL contacts potentially blocking the implant. Enhanced cleans for resist removal was implemented as a fix for the fail mode.
NanoProbing on 7 nm FinFET Devices in an SRAM Array: Challenges and Solutions
Authors: Qiu Anqi , Lowe William , Arora Mridul
Published: December 2020

Nanoprobing systems have evolved to meet the challenges from recent innovations in the semiconductor manufacturing process. This is demonstrated through an exhibition of standard SRAM measurements on TSMC 7 nm FinFET technology. SEM based nanoprober is shown to meet or exceed the requirements for measuring 7nm technology and beyond. This paper discusses in detail of the best-known methods for nanoprobing on 7nm technology.
Nanoprobing of Advanced Silicon-On-Insulator Transistors
Authors: Larentis Stefano , Erington Kent , Garcia Jose Z. , Ly Khiem , Dickson Kris , Chrastecky Tony , Heineke Steve , Gomez Nelson , Subramanian Sam
Published: December 2020

As advanced silicon-on-insulator (SOI) technology becomes a more widespread technology offering, failure analysis approaches should be adapted to new device structures. We review two nanoprobing case studies of advanced SOI technology, detailing the electrical characterization of a compound gate-to-drain defect as well as the characterization of unexpected SOI source-to-well leakage.
Statistical Failure Analysis for Non-Parametric Characteristic in DRAM
Authors: Oak Myunghoon , Lee Jongbum , Bae Jungwon , Kyungrak-Cho  , Minju-Shin  , Park Choongsun , Park Sunghoon , Hwang Hongsun , Oh Taeyoung , Kim Jonghoon , Lee Jungbae
Published: December 2020

Rapid and accurate root cause analysis of the defect contributes to improvement in yield and quality in semiconductor manufacturing system. In particular, imperfection of final test can cause major problems for customers, so analysis on root cause of final test failure is important activity for high quality. It can be started with finding first test data which is highly correlated with final test failure. However, it is difficult to analyze the correlation of first test data and final test failures because the first test is made up of hundreds of test items, and the data also show non-parametric characteristics with extreme outlier. In this study, Kolmogorov-Smirnov test (K-S test), which is a non-parametric test method, is statistically applied to the first test data. The K-S test is intuitive and descriptive, which makes it easy to analyze the root cause. And K-S test showed a performance improvement compared to t-test statistic, which requires a normal distribution assumption. Therefore, our data mining approach can help analysis to improve yield and quality of mass production with highly scaled devices.
Analisis Pengaruh Geometrik Dan Kelengkapan Rambu Lalu Lintas Terhadap Kecelakaan (Studi Kasus : Tanjakan Kethekan Kec. Jambu, Ruas Jalan Ambarawa – Magelang Km. 46+000 S/D 46+750)
Authors: Perdana Rizqi Rangga , Permata Yeremia Kristian Adi , Latifah Siti , Sukoyo Sukoyo , Wasino Wasino
Published: December 2020

Ambarawa – Magelang main road is an arterial road which used by drivers who came from Central Java headed to Yogyakarta. The Road Segment is considered to have frequent traffic accidents. The study aims to analyze the relationship between geometric aspects and the occurrence of accidents, compare actual speed with plan speed, and analyzing the completeness of the traffic signs on this section to identify the causes of accidents that occurred at that location. The stages of analysis is by doing the geometric calculation of the road and compared with the requirements in the regulation then identifying whether there is a relationship between accidents that occur with geometric conditions, vehicle speed, and the signs completeness. Identification and results of geometric analysis is known that Black Spot are on bend road I (km 46+300) there were 22 accidents due to breaking road markings, 6 accidents due to extreme bend, and 4 accidents due to road slackness throughout 2012 – 2018. On the bend road II (km 46+440) there were 5 accidents due to breaking road markings and on the bend road III (km 46+520) there were 3 accidents due to road slackness. with the result that there is a relationship between geometric conditions with accidents that occur and after being analyzed the completeness of the traffic signs is still lacking and needs to be completed.
Cyp2C19*2 Polymorphism Related to Clopidogrel Resistance in Patients With Coronary Heart Disease, Especially in the Asian Population: A Systematic Review and Meta-Analysis
Authors: Sun Ying , Lu Qing , Tao Xuefei , Cheng Biao , Yang Guoxing
Published: December 2020

In recent years, the relationship betweenCyp2C19*2 gene polymorphism and clopidogrel resistance reflected by platelet function assay has been studied extensively, but there is no clear conclusion yet. In order to evaluate the relationship betweenCyp2C19*2 gene polymorphism and clopidogrel resistance more accurately, meta-analysis was conducted in this study. The I2value taking 50% as the limit, the heterogeneity is judged as high or low, and then a random effect model or a fixed effect model is selected for statistical analysis. PubMed, EMBASE, Web of Science, CNKI, and China Wanfang database were searched, and the related literatures from the establishment of the database to May 2020 were collected and analyzed by STATA 15.0 software. A total of 3,073 patients were involved in 12 studies, including 1,174 patients with clopidogrel resistance and 1,899 patients with non-clopidogrel resistance. The results of this study showed that allele model (A vs. G): OR = 2.42 (95%CI: 1.97–2.98); dominant model (AA+GA vs. GG): OR = 2.74 (95%CI: 2.09–3.59); recessive model (AA vs. GA+GG): OR = 4.07 (95%CI: 3.06–5.41); homozygous model (AA vs. GG): OR = 5.70 (95%CI: 4.22–7.71); heterozygote model (GA vs. GG): OR = 2.32 (95%CI: 1.76–3.07), the differences were statistically significant. Also, the analysis of the Ethnicity subgroup indicated that the Asian allele model and the other four gene models were statistically significant. In conclusion,Cyp2C19*2 gene polymorphism is strongly associated with clopidogrel resistance. Allele A, genotype GA, AA, and GG + GA can increase clopidogrel resistance, especially in the Asian population.
The Roles of Stroma-Derived Chemokine in Different Stages of Cancer Metastases
Authors: Hussain Shahid , Peng Bo , Cherian Mathew , Song Jonathan W. , Ahirwar Dinesh K. , Ganju Ramesh K.
Published: December 2020

The intricate interplay between malignant cells and host cellular and non-cellular components play crucial role in different stages of tumor development, progression, and metastases. Tumor and stromal cells communicate to each other through receptors such as integrins and secretion of signaling molecules like growth factors, cytokines, chemokines and inflammatory mediators. Chemokines mediated signaling pathways have emerged as major mechanisms underlying multifaceted roles played by host cells during tumor progression. In response to tumor stimuli, host cells-derived chemokines further activates signaling cascades that support the ability of tumor cells to invade surrounding basement membrane and extra-cellular matrix. The host-derived chemokines act on endothelial cells to increase their permeability and facilitate tumor cells intravasation and extravasation. The tumor cells-host neutrophils interaction within the vasculature initiates chemokines driven recruitment of inflammatory cells that protects circulatory tumor cells from immune attack. Chemokines secreted by tumor cells and stromal immune and non-immune cells within the tumor microenvironment enter the circulation and are responsible for formation of a “pre-metastatic niche” like a “soil” in distant organs whereby circulating tumor cells “seed’ and colonize, leading to formation of metastatic foci. Given the importance of host derived chemokines in cancer progression and metastases several drugs like Mogamulizumab, Plerixafor, Repertaxin among others are part of ongoing clinical trial which target chemokines and their receptors against cancer pathogenesis. In this review, we focus on recent advances in understanding the complexity of chemokines network in tumor microenvironment, with an emphasis on chemokines secreted from host cells. We especially summarize the role of host-derived chemokines in different stages of metastases, including invasion, dissemination, migration into the vasculature, and seeding into the pre-metastatic niche. We finally provide a brief description of prospective drugs that target chemokines in different clinical trials against cancer.
Protein Disulfide Isomerases Regulate IgE-Mediated Mast Cell Responses and Their Inhibition Confers Protective Effects During Food Allergy
Authors: Krajewski Dylan , Polukort Stephanie H. , Gelzinis Justine , Rovatti Jeffrey , Kaczenski Edwin , Galinski Christine , Pantos Megan , Shah Nickul N. , Schneider Sallie S. , Kennedy Daniel R. , Mathias Clinton B.
Published: December 2020

The thiol isomerase, protein disulfide isomerase (PDI), plays important intracellular roles during protein folding, maintaining cellular function and viability. Recent studies suggest novel roles for extracellular cell surface PDI in enhancing cellular activation and promoting their function. Moreover, a number of food-derived substances have been shown to regulate cellular PDI activity and alter disease progression. We hypothesized that PDI may have similar roles during mast cell-mediated allergic responses and examined its effects on IgE-induced mast cell activity during cell culture and food allergy. Mast cells were activatedviaIgE and antigen and the effects of PDI inhibition on mast cell activation were assessed. The effects of PDI blockadein vivowere examined by treating mice with the irreversible PDI inhibitor, PACMA-31, in an ovalbumin-induced model of food allergy. The role of dietary PDI modulators was investigated using various dietary compounds including curcumin and quercetin-3-rutinoside (rutin). PDI expression was observed on resting mast cell surfaces, intracellularly, and in the intestines of allergic mice. Furthermore, enhanced secretion of extracellular PDI was observed on mast cell membranes during IgE and antigen activation. Insulin turbidimetric assays demonstrated that curcumin is a potent PDI inhibitor and pre-treatment of mast cells with curcumin or established PDI inhibitors such as bacitracin, rutin or PACMA-31, resulted in the suppression of IgE-mediated activation and the secretion of various cytokines. This was accompanied by decreased mast cell proliferation, FcεRI expression, and mast cell degranulation. Similarly, treatment of allergic BALB/c mice with PACMA-31 attenuated the development of food allergy resulting in decreased allergic diarrhea, mast cell activation, and fewer intestinal mast cells. The production of TH2-specific cytokines was also suppressed. Our observations suggest that PDI catalytic activity is essential in the regulation of mast cell activation, and that its blockade may benefit patients with allergic inflammation.
RNA Vaccines: A Suitable Platform for Tackling Emerging Pandemics?
Authors: Sandbrink Jonas B. , Shattock Robin J.
Published: December 2020

The COVID-19 pandemic demonstrates the ongoing threat of pandemics caused by novel, previously unrecognized, or mutated pathogens with high transmissibility. Currently, vaccine development is too slow for vaccines to be used in the control of emerging pandemics. RNA-based vaccines might be suitable to meet this challenge. The use of an RNA-based delivery mechanism promises fast vaccine development, clinical approval, and production. The simplicity of in vitro transcription of mRNA suggests potential for fast, scalable, and low-cost manufacture. RNA vaccines are safe in theory and have shown acceptable tolerability in first clinical trials. Immunogenicity of SARS-CoV-2 mRNA vaccines in phase 1 trials looks promising, however induction of cellular immunity needs to be confirmed and optimized. Further optimization of RNA vaccine modification and formulation to this end is needed, which may also enable single injection regimens to be achievable. Self-amplifying RNA vaccines, which show high immunogenicity at low doses, might help to improve potency while keeping manufacturing costs low and speed high. With theoretical properties of RNA vaccines looking promising, their clinical efficacy is the key remaining question with regard to their suitability for tackling emerging pandemics. This question might be answered by ongoing efficacy trials of SARS-CoV-2 mRNA vaccines.
Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of “Candidatus Desulfomonile Palmitatoxidans”
Authors: Alves Joana I. , Salvador Andreia F. , Castro A. Rita , Zheng Ying , Nijsse Bart , Atashgahi Siavash , Sousa Diana Z. , Stams Alfons J. M. , Alves M. Madalena , Cavaleiro Ana J.
Published: December 2020

Microbial communities with the ability to convert long-chain fatty acids (LCFA) coupled to sulfate reduction can be important in the removal of these compounds from wastewater. In this work, an enrichment culture, able to oxidize the long-chain fatty acid palmitate (C16:0) coupled to sulfate reduction, was obtained from anaerobic granular sludge. Microscopic analysis of this culture, designated HP culture, revealed that it was mainly composed of one morphotype with a typical collar-like cell wall invagination, a distinct morphological feature of theDesulfomonilegenus. 16S rRNA gene amplicon and metagenome-assembled genome (MAG) indeed confirmed that the abundant phylotype in HP culture belong toDesulfomonilegenus [ca.92% 16S rRNA gene sequences closely related toDesulfomonilespp.; andca. 82% whole genome shotgun (WGS)]. Based on similar cell morphology and average nucleotide identity (ANI) (77%) between theDesulfomonilesp. in HP culture and the type strainDesulfomonile tiedjeistrain DCB-1T, we propose a novel species designated as “CandidatusDesulfomonile palmitatoxidans.” This bacterium shares 94.3 and 93.6% 16S rRNA gene identity withDesulfomonile limimarisstrain DCB-MTandD. tiedjeistrain DCB-1T, respectively. Based on sequence abundance ofDesulfomonile-morphotype in HP culture, its predominance in the microscopic observations, and presence of several genes coding for enzymes involved in LCFA degradation, the proposed species “Ca.Desulfomonile palmitatoxidans” most probably plays an important role in palmitate degradation in HP culture. Analysis of the growth of HP culture andD. tiedjeistrain DCB-1Twith short- (butyrate), medium- (caprylate) and long-chain fatty acids (palmitate, stearate, and oleate) showed that both cultures degraded all fatty acids coupled to sulfate reduction, except oleate that was only utilized by HP culture. In the absence of sulfate, neither HP culture, norD. tiedjeistrain DCB-1Tdegraded palmitate when incubated withMethanobacterium formicicumas a possible methanogenic syntrophic partner. UnlikeD. tiedjeistrain DCB-1T, “Ca.Desulfomonile palmitatoxidans” lacks reductive dehalogenase genes in its genome, and HP culture was not able to grow by organohalide respiration. An emended description of the genusDesulfomonileis proposed. Our study reveals an unrecognized LCFA degradation feature of theDesulfomonilegenus.
From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies
Authors: Jauss Robin-Tobias , Walden Susanne , Fiore-Donno Anna Maria , Dumack Kenneth , Schaffer Stefan , Wolf Ronny , Schlegel Martin , Bonkowski Michael
Published: December 2020

Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.
Novel Opportunity to Reverse Antibiotic Resistance: To Explore Traditional Chinese Medicine With Potential Activity Against Antibiotics-Resistance Bacteria
Authors: Su Ting , Qiu Ye , Hua Xuesi , Ye Bi , Luo Haoming , Liu Da , Qu Peng , Qiu Zhidong
Published: December 2020

Antibiotic resistance is becoming significantly prominent and urgent in clinical practice with the increasing and wide application of antibacterial drugs. However, developing and synthesizing new antimicrobial drugs is costly and time-consuming. Recently, researchers shifted their sights to traditional Chinese medicine (TCM). Here, we summarized the inhibitory mechanism of TCM herbs and their active ingredients on bacteria, discussed the regulatory mechanism of TCM on antibiotic-resistant bacteria, and revealed preclinical results of TCM herbs and their active components against antibiotic-resistant bacteria in mouse models. Those data suggest that TCM herbs and their effective constituents exhibit potential blockage ability on antibiotic-resistant bacteria, providing novel therapeutic ideas for reversing antibiotic resistance.
Quantification of Blood Caffeine Levels in Patients With Parkinson's Disease and Multiple System Atrophy by Caffeine ELISA
Authors: Ohmichi Takuma , Kasai Takashi , Shinomoto Makiko , Matsuura Jun , Koizumi Takashi , Kitani-Morii Fukiko , Tatebe Harutsugu , Sasaki Hidenao , Mizuno Toshiki , Tokuda Takahiko
Published: December 2020

Caffeine is considered to be a neuroprotective agent against Parkinson's disease (PD) and is expected to offer a blood-based biomarker for the disease. We herein investigated the ability of this biomarker to discriminate between PD and neurodegenerative diseases. To quantify caffeine concentrations in serum and plasma, we developed a specific competitive enzyme-linked immunosorbent assay (ELISA). To validate the diagnostic performance of the assay, we conducted a case control-study of two independent cohorts among controls and patients with PD and multiple system atrophy (MSA). Parallelism, recovery rate, and intra- and inter-assay precision of our assay were within the standard of acceptance. In the first cohort of 31 PD patients, 18 MSA patients and 33 age-matched controls, serum caffeine levels were significantly lower in PD patients than in Controls (p = 0.018). A similar trend was also observed in the MSA group, but did not reach the level of significance. In the second cohort of 50 PD patients, 50 MSA patients and 45 age-matched controls, plasma caffeine levels were significantly decreased in both PD and MSA groups compared to Controls (p < 0.001). This originally developed ELISA offered sufficient sensitivity to detect caffeine in human serum and plasma. We reproducibly confirmed decreased blood concentrations of caffeine in PD compared to controls using this ELISA. A similar trend was observed in the MSA group, despite a lack of consistent significant differences across cohorts.
Biophysical Characterization of a Novel SCN5A Mutation Associated With an Atypical Phenotype of Atrial and Ventricular Arrhythmias and Sudden Death
Authors: Ghovanloo Mohammad-Reza , Atallah Joseph , Escudero Carolina A. , Ruben Peter C.
Published: December 2020

Background

Sudden cardiac death (SCD) is an unexpected death that occurs within an hour of the onset of symptoms. Hereditary primary electrical disorders account for up to 1/3 of all SCD cases in younger individuals and include conditions such as catecholaminergic polymorphic ventricular tachycardia (CPVT). These disorders are caused by mutations in the genes encoding cardiac ion channels, hence they are known as cardiac channelopathies. We identified a novel variant, T1857I, in the C-terminus of Nav1.5 (SCN5A) linked to a family with a CPVT-like phenotype characterized by atrial tachy-arrhythmias and polymorphic ventricular ectopy occurring at rest and with adrenergic stimulation, and a strong family history of SCD.

Objective

Our goal was to functionally characterize the novel Nav1.5 variant and determine a possible link between channel gating and clinical phenotype.

Methods

We first used electrocardiogram recordings to visualize the patient cardiac electrical properties. Then, we performed voltage-clamp of transiently transfected CHO cells. Lastly, we used the ventricular/atrial models to visualize gating defects on cardiac excitability.

Results

Voltage-dependences of both activation and inactivation were right-shifted, the overlap between activation and inactivation predicted increased window currents, the recovery from fast inactivation was slowed, there was no significant difference in late currents, and there was no difference in use-dependent inactivation. The O’Hara-Rudy model suggests ventricular after depolarizations and atrial Grandi-based model suggests a slight prolongation of atrial action potential duration.

Conclusion

We conclude that T1857I likely causes a net gain-of-function in Nav1.5 gating, which may in turn lead to ventricular after depolarization, predisposing carriers to tachy-arrhythmias.
Suitability of Composting Process for the Disposal and Valorization of Brewer’s Spent Grain
Authors: Assandri Davide , Pampuro Niccolò , Zara Giacomo , Cavallo Eugenio , Budroni Marilena
Published: December 2020

The brewing industry is characterized by the large production of by-products. Following the fundamentals of a circular economy, several attempts to recycle brewers’ spent grain (BSG) have been investigated. However, little information is available on its use for composting. Considering the main parameters required for optimal development of composting, the objective of the present review was to analyze the literature to determine whether the microbial and physicochemical characteristics of BSG make it suitable for direct composting. As the main factors in the composting process, we considered the BSG moisture content, total carbon, total nitrogen, C/N ratio, and pH. As described in the literature, the BSG moisture content, C/N ratio, and pH range from 70.6% to 81.3%, 7.1 to 26.5, and 3.8 to 6.9, respectively. This C/N ratio range is lower than the composting target range (20–30). Instead, the mean moisture content in the literature is higher than the 60% to 65% recommended for composting. Optimum pH for aerobic stabilization of compost ranges from 5.5 to 7.5, while the BSG pH in the literature is typically more acidic. Therefore, BSG is not suitable for direct composting. Addition of lignocellulosic bulking agents improves the reduction of moisture content during composting, while also optimizing the substrate properties, such as C/N ratio, air spaces, and pH, to positively affect the composting process. Moreover, livestock manure should be included as a starting material to promote the composting process. In this context, two hypothetical initial mixtures of BSG plus a lignocellulosic bulking agent and livestock manure are presented.
Performance and Milk Composition of Nubian Goats as Affected by Increasing Level of Nannochloropsis oculata Microalgae
Authors: Kholif Ahmed E. , Gouda Gouda A. , Hamdon Hatem A.
Published: December 2020

Fat supplementation affects the lactational performance of goats and dramatically changes milk nutritive value. In the present experiment, two levels of Nannochloropsis oculata microalgae, a natural source of rumen-protected eicosapentaenoic acid (EPA), were studied in the diet of Nubian goats. Using quintuplicated 3 × 3 Latin square design, fifteen lactating goats, (14 ± 2 months old and 33.0 ± 1.3 kg) after kidding, were randomly assigned into three treatments in an 84-d assay. Goats were offered a basal diet comprising berseem clover, wheat straw and concentrates in 3:2:5, respectively, (control treatment-no supplementation). The other two treatments were supplemented with N. oculata microalgae at 5 g (NOM5 treatment) or 10 g (NOM10 treatment)/doe/d. Without affecting intake, treatments improved (p < 0.01) nutrient digestibility. Supplementations had no effect on ruminal pH and ammonia-nitrogen, however, NOM5 and NOM10 linearly improved (p < 0.05) total volatile fatty acids and propionic acids. N. oculata supplementation linearly increased (p < 0.01) milk yield and lactose content. Supplementation reduced atherogenic index (p = 0.004) and enhanced the concentrations of unsaturated fatty acids and C20:5n3 (EPA). Conclusively, feeding Nubian goats on diet supplemented with N. oculata at 5 and 10 g improved milk production and the nutritive value. No improvements in the performance were observed when N. oculata dose was increased from 5 g to 10 g/doe; thus, 5 g dose is recommended for use.
Multienzyme Super-Dosing in Broiler Chicken Diets: The Implications for Gut Morphology, Microbial Profile, Nutrient Digestibility, and Bone Mineralization
Authors: Madigan-Stretton Jacoba , Mikkelsen Deirdre , Soumeh Elham Assadi
Published: December 2020

Optimizing gut health has a large impact on nutrient digestibility and bioavailability, and super-dosing feed enzymes may be one solution to achieve this. A 42-day grow-out trial was conducted using 192 Ross 308 broilers to determine if super-dosing Natuzyme at 0 g/t, 350 g/t, 700 g/t, and 1000 g/t dose rates could improve the gut morphology, alter the cecal microbial profile, enhance bone mineralization, and improve nutrient digestibility of a wheat–corn–soybean diet (six replicates per treatment, eight birds per pen). One bird per pen was slaughtered at day 42 and gut morphology, cecal microbial profile, and nutrient digestibility were studied. The addition of enzymes tended to increase the villus height in the duodenum, villus height, width, and crypt depth in the jejunum, and villus width and the number of goblet cells in the ileum. Microbial profiling revealed diverse communities; however, they did not significantly differ between treatment groups. Yet, 700 g/t Natuzyme promoted microbes belonging to the genus Romboutsia and Ruminococcus gauvreauii, while 1000 g/t Natuzyme promoted Barnesiella species. The nutrient digestibility demonstrated a significant improvement in all enzyme doses compared to the control. In conclusion, based on the outcomes of this study, a dose rate of 700 g/t Natuzyme is recommended to improve gut morphology and nutrient digestibility, and promote unique microbes which aid in feed efficiency.
Prevalence, Antimicrobial Susceptibility, Virulence and Genotyping of Campylobacter jejuni with a Special Reference to the Anti-Virulence Potential of Eugenol and Beta-Resorcylic Acid on Some Multi-Drug Resistant Isolates in Egypt
Authors: Ammar Ahmed M. , El-Naenaeey El-Sayed Y. , El-Malt Rania M. S. , El-Gedawy Attia A. , Khalifa Eman , Elnahriry Shimaa S. , Abd El-Hamid Marwa I.
Published: December 2020

Campylobacter jejuni is the leading cause of foodborne bacterial gastroenteritis in humans worldwide. Contaminated chickens and their products are the main sources of human campylobacteriosis. Therefore, this study aimed to detect the genotypic and virulence genes‘ profiles of multi-drug resistant (MDR) C. jejuni isolates and to assess the effects of sub-inhibitory concentrations (SICs) of eugenol and beta-resorcylic acid on the virulence of avian MDR C. jejuni isolates. These isolates were clustered together with the human isolates via enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) fingerprinting. A total of 345 samples were collected from human stool (100) and different chicken (245) samples in Sharkia Governorate, Egypt. Conventional phenotypic methods identified 113 isolates (32.8%) as C. jejuni, and all C. jejuni isolates were MDR and resistant to erythromycin and ampicillin. The genes virB11, wlaN, and flaA were detected in 52%, 36% and 100% strains, respectively. ERIC-PCR yielded 14 profiles and five main clusters. Interestingly, human and chicken C. jejuni isolates were clustered together in ERIC-PCR clusters II-V, which confirmed the genetic relatedness between the isolates from both origins. Beta-resorcylic acid and eugenol inhibited the invasion of C. jejuni isolates to chicken intestinal cells by 41.66–38.19% and 31.94–29.16%, respectively, and minimized the transcription of flaA, virB11, and wlaN genes in the tested isolates by real-time quantitative reverse transcription PCR (qRT-PCR). In essence, eugenol and beta-resorcylic acid are promising natural antimicrobials for minimizing the virulence of MDR C. jejuni in chickens, thereby managing human campylobacteriosis.
High Vulnerability of Oligodendrocytes to Oxidative Stress Induced by Ultrafine Urban Particles
Authors: Kim Ji Young , Kim Jin-Hee , Kim Yong-Dae , Seo Je Hoon
Published: December 2020

Oligodendrocytes, myelin-forming cells in the brain, are vulnerable to oxidative stress. Recent work indicates that air pollution causes demyelinating diseases such as multiple sclerosis. However, little is known about the mechanism of toxicity of ultrafine particulate matters (PMs) to oligodendrocytes. Here, we aimed to determine whether oligodendrocyte precursor cells (OPCs) and mature oligodendrocytes (mOLs) are more vulnerable to ultrafine urban PMs (uf-UPs) than other types of brain cells and damage to adult OPCs and mOLs in the mouse brain exposed to uf-UPs. For in vitro experiments, following exposure to various concentrations (2, 20, and 200 μg/mL) of uf-UPs, we measured survival rates, the amount of reactive oxygen species (ROS), and the total antioxidant capacities (TACs) of brain cells isolated from neonatal Sprague-Dawley rats. For animal experiments, after a four-week exposure to a uf-UP suspension (20 μL, 0.4 mg/mL), we enumerated the number of damaged cells and typed damaged cells in the white matter of the cerebellum of uf-UP-exposed mice. MTT assays and Hoechst staining demonstrated that OPCs and mOLs were more vulnerable to uf-UP-induced damage than astrocytes and cortical neurons at 2, 20, and 200 μg/mL of uf-UPs examined in this study (p < 0.05). Damage to OPCs and mOLs depended on uf-UP concentration. DCF assays and DHE staining indicated that the amount of ROS generated in OPCs and mOLs was significantly higher than in other brain cell types (p < 0.05). In contrast, TAC values in OPCs and mOLs were significantly lower than those of other brain cell types (p < 0.05). Fluoro-Jade B (FJB)-positive cells in the cerebellar white matter of the uf-UP-exposed group were significantly greater in number relative to the control group. Double immunofluorescence indicated that FJB-positive cells are NG2-positive adult OPCs and carbon anhydrase II-positive mOLs. Taken together, our findings suggest that oxidative stress induced by uf-UPs in the brain impairs adult OPCs and mOLs, causing demyelination and reducing the capacity for remyelination.
Effect of Cooking Methods on the Antioxidant Capacity of Plant Foods Submitted to In Vitro Digestion–Fermentation
Authors: Navajas-Porras Beatriz , Pérez-Burillo Sergio , Valverde-Moya Álvaro Jesús , Hinojosa-Nogueira Daniel , Pastoriza Silvia , Rufián-Henares José Ángel
Published: December 2020

The antioxidant capacity of foods is essential to complement the body’s own endogenous antioxidant systems. The main antioxidant foods in the regular diet are those of plant origin. Although every kind of food has a different antioxidant capacity, thermal processing or cooking methods also play a role. In this work, the antioxidant capacity of 42 foods of vegetable origin was evaluated after in vitro digestion and fermentation. All foods were studied both raw and after different thermal processing methods, such as boiling, grilling roasting, frying, toasting and brewing. The cooking methods had an impact on the antioxidant capacity of the digested and fermented fractions, allowing the release and transformation of antioxidant compounds. In general, the fermented fraction accounted for up to 80–98% of the total antioxidant capacity. The most antioxidant foods were cocoa and legumes, which contributed to 20% of the daily antioxidant capacity intake. Finally, it was found that the antioxidant capacity of the studied foods was much higher than those reported by other authors since digestion–fermentation pretreatment allows for a higher extraction of antioxidant compounds and their transformation by the gut microbiota.