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Additional file 1. Boundaries of linkage disequilibrium between a QTL and a SNP with different MAF. This file provides derivation and simulation results for boundaries of linkage disequilibrium between a QTL and a SNP with different MAF.

Genomic prediction uses a reference population of animals with SNP genotypes and phenotypes to predict the merit of selection candidates that typically do not have observed phenotypes. Accuracy of genomic prediction from models that fitted 50K SNP genotypes was low when selection candidates were from a breed only distantly related with the breeds in the reference population. That accuracy was not improved by increasing SNP density from 50K to a ten-fold higher density using imputation. This indicates that the accuracy of genomic prediction mainly came from family-wise co-segregation information. In this study, a genomic prediction model that fitted genome-wide 100 kilo-bp (Kbp) haplotypes improved accuracy for breeds that were not in the reference population. The haplotype model is a more accurate alternative to the SNP model for genomic prediction when animals of the same breed as the prediction candidates are not available for the reference population.

Electronic–photonic synergy has become an increasingly clear solution to enhance the bandwidth and improve the energy efficiency of information systems. Monolithic integration of optoelectronic devices is the ideal solution for large-scale electronic–photonic synergy. Due to its pseudo-direct gap behavior in optoelectronic properties and compatibility with Si electronics, epitaxial Ge-on-Si has become an attractive solution for monolithic optoelectronics. In this paper we will review recent progress in Ge-on-Si optoelectronics, including photodetectors, electroabsorption modulators, and lasers. The performance of these devices has been enhanced by band-engineering such as tensile strain and n-type doping, which transforms Ge towards a direct gap material. Selective growth reduces defect density and facilitates monolithic integration at the same time. Ge-on-Si photodetectors have approached or exceeded the performance of their III–V counterparts, with bandwidth-efficiency product > 30 GHz for p-i-n photodiodes and bandwidth-gain product > 340 GHz for avalanche photodiodes. Enhanced Franz–Keldysh effect in tensile-strained Ge offers ultralow energy photonic modulation with 100 GHz intrinsic bandwidth. Room temperature optically-pumped lasing as well as electroluminescence has also been achieved from the direct gap transition of band-engineered Ge-on-Si waveguides. These results indicate that band-engineered Ge-on-Si is promising to achieve monolithic active optoelectronic devices on a Si platform.

Genomic profiling of hepatocellular carcinoma (HCC) tumors has elucidated recurrent molecular aberrations common or specific to disease etiology, patient race or geographic regions, allowing the classification of HCC tumors into subclasses sharing similar molecular and clinical characteristics. Previously reported transcriptome-based molecular subclasses have highlighted several common themes. Aggressive tumors are characterized by TP53 inactivation mutations and activation of pro-oncogenic signaling pathways, and further subclassified according to expression of stemness markers. The stemness marker-negative aggressive tumors display preferential TGF-β activation. Another group of less aggressive tumors contains a subclass characterized by CTNNB1 mutations accompanied with overexpression of liver-specific WNT targets such as GLUL. Molecular therapies selectively targeting features of the HCC subclasses have suggested their utility in enriching potential responders in clinical trials and guiding therapeutic decision-making for HCC patients.

Electronic-photonic synergy has become an increasingly clear solution to enhance the bandwidth and improve the energy efficiency of information systems. Monolithic lasers on silicon are ideal for large scale electronic-photonic integration. Germanium is a particularly interesting candidate for this application due to its pseudo-direct gap behavior in the near infrared regime for optical communications and compatibility with advanced silicon complementary metal oxide semiconductor (CMOS) technology. In this paper, we review theoretical modeling and experimental studies on optical gain and lasing from monolithic epitaxial Ge-on-Si devices band-engineered by tensile strain and n-type doping to compensate the energy difference between the direct and indirect conduction valleys. Demonstrations of optical gain and lasing at room temperature indicate that the Ge-on-Si laser is a promising candidate for monolithic electronic-photonic integrated circuits.

It has been demonstrated theoretically and experimentally that germanium, with proper strain engineering and n-type doping, can be an efficient light emitter and a gain medium at its direct bandgap within the third optical communication window ( ~1520-1620 nm). In this paper, we systematically discuss the effect of strain, doping, and temperature on the direct-gap optical gain in germanium. For electrically pumped devices, properties and design guidelines of Ge/Si heterojunction are also analyzed and compared with the results from fabricated Ge/Si heterojunction LEDs.

Thin film Ge on Si is a potential active material candidate for electrically pumped monolithically integrated Si-based light emitters. Theoretical analysis has shown that a combination of strain and n-type doping can modify the band structure of Ge so that it exhibits direct bandgap properties. Direct band-to- band optical transition is observed from the room temperature photoluminescence at around 1550nm. An optical bleaching ef- fect occurring in lock-in pump-probe measurements indicates a precursor to optical net gain.

With the emergence of genomic profiling technologies and selective molecular targeted therapies, biomarkers play an increasingly important role in the clinical management of cancer patients. Single gene/protein or multi-gene “signature”-based assays have been introduced to measure specific molecular pathway deregulations that guide therapeutic decision-making as predictive biomarkers. Genome-based prognostic biomarkers are also available for several cancer types for potential incorporation into clinical prognostic staging systems or practice guidelines. However, there is still a large gap between initial biomarker discovery studies and their clinical translation due to the challenges in the process of cancer biomarker development. In this review we summarize the steps of biomarker development, highlight key issues in successful validation and implementation, and overview representative examples in the oncology field. We also discuss regulatory issues and future perspectives in the era of big data analysis and precision medicine.

An acoustic asymmetric transmission device exhibiting unidirectional transmission property for acoustic waves is extremely desirable in many practical scenarios. Such a unique property may be realized in various configurations utilizing acoustic Zeeman effects in moving media as well as frequency-conversion in passive nonlinear acoustic systems and in active acoustic systems. Here we demonstrate a new acoustic frequency conversion process in a time-varying system, consisting of a rotating blade and the surrounding air. The scattered acoustic waves from this time-varying system experience frequency shifts, which are linearly dependent on the blade’s rotating frequency. Such scattering mechanism can be well described theoretically by an acoustic linear time-varying perturbation theory. Combining such time-varying scattering effects with highly efficient acoustic filtering, we successfully develop a tunable acoustic unidirectional device with 20 dB power transmission contrast ratio between two counter propagation directions at audible frequencies.

Background & Aims Although patients infected by genotype 1b hepatitis C virus (HCV) with Q 70 and/or M 91 core gene mutations have an almost five-fold increased risk of developing hepatocellular carcinoma (HCC) and increased insulin resistance, the absence of a suitable experimental system has precluded direct experimentation on the effects of these mutations on cellular gene expression. Methods HuH7 cells were treated long-term with human serum to induce differentiation and to produce a model system for testing high-risk and control HCV. For clinical validation, profiles of infected cells were compared to each other and to those of liver biopsies of patients with early-stage HCV-related cirrhosis followed prospectively for up to 23years (n=216). Results Long-term culture in human serum produced growth-arrested, hepatocyte-like cells whose gene profile overlapped significantly with that of primary human hepatocytes. High-risk (Q 70 /M 91 ) and control (R 70 /L 91 ) viruses had dramatically different effects on gene expression of these cells. The high-risk virus enhanced expression of pathways associated with cancer and type II diabetes, while the control virus enhanced pathways associated with oxidative phosphorylation. Of special clinical relevance, the transcriptome of cells replicating the high-risk virus correlated significantly with an HCC high-risk profile in patients (Bonferroni-corrected p =0.03), whereas no such association was observed for non-HCC-related clinical outcomes. Conclusions The cell-based system allowed direct head-to-head comparison of HCV variants, and provided experimental support for previous clinical data indicating an oncogenic effect of core gene mutations. This simple experimental system distinguished HCV variants and will enable future mechanistic analysis and exploration of interventional approaches.

To explore the timing and suitable method of reconstructing penile defects caused by devastating electrical burn.Thirteen patients with penile defects after devastating electrical burn, hospitalized from September 1998 to August 2013, were included in this study. After the necrotic tissues in the wounds were removed by dressing changes, a local or a hinge-like flap constructed from scrotum or abdominal wall, a prelaminated hinge-like flap from forearm, or a free forearm flap was selected, according to the injury degree of the penis, for the repair of the defect or reconstruction of penis respectively.The flaps survived and the wounds healed well in 2 patients repaired with local flaps from scrotum or abdominal wall. Urethritis occurred in 2 patients 6 to 9 months after the transplantation of hinge-like flaps from scrotum, and they were cured by appropriate drugs. Functions of urination and erection of penis were recovered in these 4 patients. All flaps survived in the 5 patients repaired with hinge-like flaps from abdominal wall or prelaminated flaps from forearm. The wounds in 2 patients healed; wound dehiscence occurred in the other 3 patients in different degrees, and they healed after suturing for 2 or 3 times. The function of erection of penis recovered in these 5 patients, but with discontinuity of urinary stream during urination. Among them, 3 married patients enjoyed satisfactory sexual life. All free forearm flaps survived and the wounds healed well in 4 patients. Urinary fistula occurred in 1 patient, and it was repaired by a secondary operation. These 4 patients experienced normal urination function, but only 2 patients in whom corpus spongiosum partially remained retained the function of erection of penis to certain degree. All these 4 patients could not perform normal sexual intercourse. All patients were followed up for 6 to 13 months after surgery. Under ordinary state, the length of penis was 5.9-9.3 cm, and the circumference of penis was 8.4-10.0 cm. Wound scar was not obvious in all cases. Nine patients reported a restricted erection.Penile defect caused by devastating electrical burn should be repaired with a suitable flap after necrotic tissues are removed with dressing change. To repair affected penis with necrosis of a small part of cavernous body and/or corpus spongiosum, or combined with urethra defects, local flaps from scrotum or abdominal wall or hinge-like flap from scrotum should be employed. To repair those with necrosis of a large part or the whole of corpus spongiosum combined with urethra defects, hinge-like skin flaps from abdominal wall or prelaminated flaps from forearm should be employed. In patients with necrosis of a large part of cavernous body and corpus spongiosum combined with urethra defect, or total loss of penis, free forearm flaps should be employed to reconstruct penis.

A compact parallel optical engine platform using Si optical bench technology to realize highly manufacturable vertical coaxial alignment approach is demonstrated and an in-production 40G optical engine using this platform is presented.

Background & Aims Rapid induction of β-PDGF receptor (β-PDGFR) is a core feature of hepatic stellate cell activation, but its cellular impact in vivo is not well characterized. We explored the contribution of β-PDGFR-mediated pathway activation to hepatic stellate cell responses in liver injury, fibrogenesis, and carcinogenesis in vivo using genetic models with divergent β-PDGFR activity, and assessed its prognostic implications in human cirrhosis. Methods The impact of either loss or constitutive activation of β-PDGFR in stellate cells on fibrosis was assessed following carbon tetrachloride (CCl 4 ) or bile duct ligation. Hepatocarcinogenesis in fibrotic liver was tracked after a single dose of diethylnitrosamine (DEN) followed by repeated injections of CCl 4 . Genome-wide expression profiling was performed from isolated stellate cells that expressed or lacked β-PDGFR to determine deregulated pathways and evaluate their association with prognostic gene signatures in human cirrhosis. Results Depletion of β-PDGFR in hepatic stellate cells decreased injury and fibrosis in vivo , while its auto-activation accelerated fibrosis. However, there was no difference in development of DEN-induced pre-neoplastic foci. Genomic profiling revealed ERK, AKT, and NF-κB pathways and a subset of a previously identified 186-gene prognostic signature in hepatitis C virus (HCV)-related cirrhosis as downstream of β-PDGFR in stellate cells. In the human cohort, the β-PDGFR signature was not associated with HCC development, but was significantly associated with a poorer outcome in HCV cirrhosis. Conclusions β-PDGFR is a key mediator of hepatic injury and fibrogenesis in vivo and contributes to the poor prognosis of human cirrhosis, but not by increasing HCC development.

The rate of hepatitis C virus (HCV) related liver cirrhosis and subsequent cancer development is increasing and raising the risk of related mortality and morbidity. To address this issue, we aimed to develop a prognostic index that can be used to stratify patients for risk of disease progression. This index was developed in part by using a gene signature test implemented in a clinically applicable digital transcript counting platform (NanoString nCounter system). A cohort of 145 U.S. patients with HCV-related early-stage cirrhosis was analyzed by using the assay. This dataset (GEO accession number GPL17230) provides information of expression levels of the prognostic genes in the cohort.

There is an increasing demand to determine the clinical implication of experimental findings in molecular biomedical research. Survival (or failure time) analysis methodologies have been adapted to the analysis of genomics data to link molecular information with clinical outcomes of interest. Genome-wide molecular profiles have served as sources for discovery of predictive/prognostic biomarkers as well as therapeutic targets in the past decade. In this review, we overview currently available software, web applications, and databases specifically developed for survival analysis in genomics research and discuss issues in assessing clinical utility of molecular features derived from genomic profiling.

Selenium dioxide nanowires were fabricated as the co-products of ZnSe nanostructures. The SeO2 nanowires have diameters between 20∼70 nm and lengths up to several hundred micrometers. The morphology and microstructure of the nanowires were analyzed using TEM, and the growth mechanism of the SeO2 nanowires was explained under the framework of a vapor-solid model, in which structure defects may play a very important role in the nanowire growth. The nanostructured SeO2 materials may find application in both catalytic and biological fields.

ZnO nanorod arrays have been grown on glass substrates. X-ray diffraction demonstrated that most of the nanorods in the arrays are of wurtzite crystal structure with preferable [0 0 1] growth direction. The morphology and the microstructure of the arrays and the nanorods were investigated by using scanning electron microscopy and transmission electron microscopy. A wetting layer of ZnO was observed between the nanorods and the substrate. On the (0 0 1) surfaces of some nanorods, the initial stage of nucleation and the subsequent development of the nuclei were observed, revealing the process of the nanorod growth. Electron energy-dispersive X-ray spectroscopy revealed that the wetting layer and the nanorods exhibit different stoichiometric ratio. The kinetics of the formation of the structures was discussed within the framework of the Stranski–Krastanov mechanism. In addition, photoluminescence spectra of the as-grown ZnO nanorod arrays indicate their possible applications in ultraviolet (UV) emission devices.

ZnO nanorod arrays with peculiar morphologies were synthesized on (111)-oriented Si substrate and glass via a vapor phase growth. The morphology of the individual nanorod can be flat-headed bottle-like, and needle-like, which depends on the deposition positions relative to the source materials in the presence of a controlling element Se. In addition, the arrays of all the three morphologies exhibit good alignment and high coverage. This fabrication technique can be also used to direct the controllable growth of other nanomaterials with similar morphologies.

Nitric oxide (NO), a gaseous neurotransmitter, has been implicated in the pathogenesis of schizophrenia. Accordingly, several polymorphisms of the gene that codes for the main NO-producing enzyme, the nitric oxide synthase 1 (NOS1), have been found to convey a risk for schizophrenia. This study examined the role of NOS1 gene polymorphisms in cognitive functions and related neural mechanism. First, with a sample of 580 schizophrenia patients and 720 healthy controls, we found that rs3782206 genotype had main effects on the 1-back task (P=0.005), the 2-back task (P=0.049), the AY condition of the dot-pattern expectancy (DPX) task (P=0.001), and the conflict effect of the attention network (ANT) test (P

SummaryElucidating the determinants of aggressiveness in lethal prostate cancer may stimulate therapeutic strategies that improve clinical outcomes. We used experimental models and clinical databases to identify GATA2 as a regulator of chemotherapy resistance and tumorigenicity in this context. Mechanistically, direct upregulation of the growth hormone IGF2 emerged as a mediator of the aggressive properties regulated by GATA2. IGF2 in turn activated IGF1R and INSR as well as a downstream polykinase program. The characterization of this axis prompted a combination strategy whereby dual IGF1R/INSR inhibition restored the efficacy of chemotherapy and improved survival in preclinical models. These studies reveal a GATA2-IGF2 aggressiveness axis in lethal prostate cancer and identify a therapeutic opportunity in this challenging disease.

A high bandwidth density chip-to-chip optical interconnect architecture is analyzed. The interconnect design leverages our recently developed flexible substrate integration technology to circumvent the optical alignment requirement during packaging. Initial experimental results on fabrication and characterization of the flexible photonic platform are also presented.

Artificial honeycomb lattices with Dirac cone dispersion provide a macroscopic platform to study the massless Dirac quasiparticles and their novel geometric phases. In this paper, a quadruple-degenerate state is achieved at the center of Brillouin zone (BZ) in a two-dimensional honeycomb lattice phononic crystal, which is a result of accidental degeneracy of two double-degenerate states. In the vicinity of the quadruple-degenerate state, the dispersion relation is linear. Such quadruple degeneracy is analyzed by rigorous representation theory of groups. Using method, a reduced Hamiltonian is obtained to describe the linear Dirac dispersion relations of such quadruple-degenerate state, which is well consistent with the simulation results. Near such accidental degeneracy, we observe some unique wave propagating properties, such as defect insensitive propagating character and Talbot effect., 24 pages, 7 figures and 1 table

A more nuanced approach to drug design is to use multiple drugs in combination to target interacting or complementary pathways. Drug combination treatments have shown higher efficacy, fewer side effects, and less toxicity compared to single-drug treatment. In this Review, we focus on the use of high-throughput biological measurements (genetics, transcripts, and chemogenetic interactions) and the computational methods they necessitate to further combinatorial drug design (CDD). We highlight the state-of-the-art analytical methods, including network analysis, integrative informatics, and dynamic molecular modeling, that have been used successfully in CDD. Finally, we present an exhaustive list of the publicly available data and methodological resources available to the community. Such next-generation technologies that enable the measurement of millions of cellular data points simultaneously may usher in a new paradigm in drug discovery, where medicine is viewed as a system of interacting genes and pathways rather than the result of an individual protein or gene.

We report an above-band-gap radiative transition in the photoluminescence spectra of single crystalline Ge in the temperature range of 20~296 K. The temperature-independence of the peak position at ~0.74 eV is remarkably different from the behavior of direct and indirect gap transitions in Ge. This transition is observed in n-type, p-type, and intrinsic single crystal Ge alike, and its intensity decreases with the increase of temperature with a small activation energy of 56 meV. Some aspects of the transition are analogous to III-V semiconductors with dilute nitrogen doping, which suggests that the origin could be related to an isoelectronic defect.

The SNP rs2958182 was reported to be significantly associated with schizophrenia (SCZ) in Han Chinese. This study examined this SNP's associations with cognitive functions in 580 SCZ patients and 498 controls. Cognitive functions were assessed using the Wechsler Adult Intelligence Scale-Revised (WAIS-RC), the Attention Network Task (ANT), the Stroop task, the dot pattern expectancy (DPX), task and the N-back working memory task. Results showed significant or marginally significant interaction effects between genotype and diagnosis status on IQ (P=0.011) and attention-related tasks (ie, the forward digit span of WAIS-RC, P=0.005; the ANT conflict effect; P=0.020, and its ratios over mean reaction time (RT), P=0.036; the Stroop conflict effect, P=0.032, and its ratios over mean RT, P=0.062; and the DPX task's error rate under the BX condition, P0.05). Further analysis of the significant genotype-by-diagnosis interactions showed that the risk (T) allele was associated with better performance on cognitive tasks in patients but with worse performance in controls. These results seem to indicate that the association between this SNP and selected cognitive functions may be of an inverted U-shaped pattern. Future research is needed to replicate these results and to explore the biochemical mechanisms behind this association. © 2013 American College of Neuropsychopharmacology. All rights reserved.

Discrete and dynamic optimization is a significant methodology that has been widely applied to operation management fields.This issue on discrete and dynamic optimization problems in operationmanagement aims at an all-around research and the state-of-the-art theoretical, numerical, and practical achievements that contribute to this field. This issue contains 21 papers, with the following features.

As uncertainties increase in both the acquisition of used products and the demand of remanufactured products, balancing supply and demand has become more important for a remanufacturing firm. Therefore, the remanufacturing firm needs to combine acquisition management with remanufacturing planning. Used products are often collected from a large number of end users, and acquisition pricing is adopted to control the return quantity of the used product. In this paper, we study a multiperiod acquisition pricing and remanufacturing decision problem under random price-sensitive returns. First, the problem is formulated into a two-decision periodic review inventory model, the decomposition property of which is proved, and thus, the problem can be decomposed into two subproblems with single decision variable. Second, we acquire the solution structure of the optimal remanufacturing quantity, which is a basic inventory policy not influenced by random returns. Next, we analyze characteristics of the optimal acquisition price and derive a monotonic pricing policy depending on the starting level of the whole inventory in each period. Further, an algorithm is designed to calculate the optimal inventory level and acquisition price of each period, which holds a lower computational complexity. Finally, numerical examples are provided to show the effectiveness of the algorithm and to conduct managerial insights of main parameters.

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Optical structures with balanced loss and gain provide an efficient platform to study the features of light propagation under non-Hermitian parity-time symmetry. Here, we report a feasible design of one-dimensional parity-time symmetric diffraction grating, where the real and imaginary parts of refractive index are separately modulated. Due to the spontaneous breaking of parity-time symmetry at the exceptional point, asymmetric diffractions are observed between a pair of oblique incident light. This asymmetric phenomenon, determined by the modulation direction of the introduced parity-time symmetry, is also polarization-dependent. The coupled-mode theory is implemented to theoretically analyze the polarization dependent asymmetric diffraction, showing consistence with numerical simulations. Our findings may provide a feasible way for manipulating light and instructively inspire the development of diffraction optics.

We report a design of topological phononic states for underwater sound using arrays of acoustic coupled ring resonators. In each individual ring resonator, two degenerate acoustic modes, corresponding to clockwise and counter-clockwise propagation, are treated as opposite pseudospins. The gapless edge states arise in the bandgap resulting in protected pseudospin-dependent sound transportation, which is a phononic analogue of the quantum spin Hall effect. We also investigate the robustness of the topological sound state, suggesting that the observed pseudospin-dependent sound transportation remains unless the introduced defects facilitate coupling between the clockwise and counter-clockwise modes (in other words, the original mode degeneracy is broken). The topological engineering of sound transportation will certainly promise unique design for next generation of acoustic devices in sound guiding and switching, especially for underwater acoustic devices.

Well-aligned arrays of ZnO nanoneedles were fabricated using a simple vapor phase growth. The diameters of the nanoneedle tips are as small as several nanometers, which is highly in favor of the field emission. Field-emission measurements using the nanoneedle arrays as cathode showed emission current density as high as 2.4 mA/cm2 under the field of 7 V/μm, and a very low turn-on field of 2.4 V/μm. Such a high emission current density is attributed to the high aspect ratio of the nanoneedles. The high emission current density, high stability, and low turn-on field make the ZnO nanoneedle arrays one of the promising candidates for field-emission displays.

Stoichiometric ZnSe nanowires have been synthesized through a vapor phase reaction of zinc and selenium powder on the (100) silicon substrate coated with a gold film of 2 nm in thickness. The microstructures and the chemical compositions of the as-grown nanowires have been investigated by means of electron microscopy, the energy dispersive spectroscopy, and Raman spectroscopy. The results reveal that the as-grown materials consist of ZnSe nanowires with diameters ranging from 5 to 50 nm. Photoluminescence of the sample demonstrates a strong green emission from room temperature down to 10 K. This is attributed to the recombination of electrons from conduction band to the medium deep Au acceptors.

With the development of the Internet, the word-of-mouth gradually achieves digital online reviews. On the one hand, enterprises can expand their cooperative marketing and set up good social image; On the other hand, the online reviews can also help customers to obtain more comprehensive information and offer more valuable information for making decision. Through the online reviews, enterprises can make full use of their advantages. Scientific management and marketing about online reviews have become the key to success of collaborative marketing for enterprises. The purpose of this paper is based on the cooperative marketing, using the AHP method to analyze how online reviews affect cooperative marketing sales change and help people understand and give full play to the influence of the online reviews. This paper can offer specific guidance for enterprises to develop effect that online reviews impose on management and marketing.

To meet the unprecedented demands for data transmission speed and bandwidth silicon integrated photonics that can generate, modulate, process and detect light signals is being developed. Integrated silicon photonics that can be built using existing CMOS fabrication facilities offers the tantalizing prospect of a scalable and cost-efficient solution to replace electrical interconnects. Silicon, together with commonly used dielectric materials in CMOS processes such as silicon dioxide, is a great material system for optical confinement and wave transmission in near infrared range. However, silicon is not a good choice for active photonic devices due to its transparency in such wavelength range. Germanium and GeSi alloy, the materials that have long been adopted to improve the performance of silicon transistors in many ways, have been showing their potential as the building blocks of such active integrated optical devices. This chapter discusses the research of using germanium and GeSi for silicon-integrated photodetection and light source in the contexts of material physics and growth, device design and fabrication. This introduction section briefly introduces the background of integrated silicon photonics and some germanium properties which are important for photonic applications. Next section focuses on waveguide-integrated germanium photodetectors which can readily be integrated with silicon waveguide on mature silicon or silicon-on-insulator (SOI) platform. The physics and design considerations of these devices are presented with details. The fabrication processes of these devices are also discussed with some extent. Next section includes a newly developed field that using germanium for light sources in silicon photonics applications such as light-emitting-diodes (LEDs) and lasers. There has been a few breakthroughs in this topic including the author’s work of epitaxial germanium LEDs and optically pumped lasers operating at room temperature. The physics of this unusual concept of using indirect band gap material for light emission is discussed in details and some important results are presented.